BCM

Cloning_Vectors

NCBI Data

Genome Projects
TA search
91 volumes: 87 with qual & 4 with no quality
85 volumes contain BCM reads
Avg LEN=984
Avg CLIP (CLB intersect CLV)=760
Avg CLV=997 (3.66M reads) !!!> Avg LEN
Avg QUAL=38.96 (27.51 for the 2.59M reads not in the UMD assembly)
0 QUAL reads 650,133

Avg UMDoverlapper CLIP=778 (3.53M reads)

CENTER_NAME counts

    COUNT           CENTER_NAME     
 1  35629020        BCM             Baylor College of Medicine
 2  737900          NISC            NIH Intramural Sequencing Center
 3  652614          BCCAGSC         British Columbia Cancer Agency Genome Sciences Centre                           # TA query_tracedb CENTER_NAME = "BCCAGSC" => 652,510 
 4  378871          MARC            USDA, ARS, US Meat Animal Research Center
 5  114753          UIUC            University of Illinois at Urbana-Champaign                                      # TA query_tracedb CENTER_NAME = "UIUC" => 106,368
 6  107367          BARC            USDA, ARS, Beltsville Agricultural Research Center
 7  65171           TIGR            The Institute for Genome Research
 8  53556           GSC             Genoscope
 9  43033           CENARGEN        Embrapa Genetic Resources and Biotechnology
 10 18623           SC              The Sanger Center
 11 15301           UOKNOR          University of Oklahoma Norman Campus, Advanced Center for Genome Technology
 12 10651           TIGR_JCVIJTC    The Institute for Genomic Research, Traces generated at JCVIJTC                 # TA query_tracedb CENTER_NAME="JCVI"
 13 2485            UIACBCB         University of Iowa Center for Bioinformatics and Computation Biology (UIACBCB)
 14 49              WUGSC           Washington University, Genome Sequencing Center                                 # TA query_tracedb CENTER_NAME = "WUGSC" => 9
    37829394        total           total                                                                           # TA query_tracedb SPECIES_CODE = "BOS TAURUS" => 37,788,710

TRACE_TYPE_CODE counts

    COUNT         CENTER_NAME     TRACE_TYPE_CODE        #LIBS(all)     #LIBS(10K+ reads)
 1  24863599      BCM*            WGS                    89             31
 2  10748529      BCM*            SHOTGUN                10             10
 3  737900        NISC            SHOTGUN                4              3
 4  125597        BCCAGSC         CLONEEND                                    large insert size; !!! all have CLIP3=0
 5  114753        UIUC            CLONEEND                                    insert size missing , no frequent kmers
 6  65171         TIGR            CLONEEND                                    2K & 2K inserts, most reads have no direction
 7  53556         GSC             CLONEEND                                    large insert size; !!! all have qual=0 and were excluded 
 8  26246         CENARGEN        WGS                                         insert size missing
 9  25454         BARC            CLONEEND                                    !!! all have CLIP3=0
 10 16892         BCM*            CLONEEND               1              1     VBBAA   mea=167000  std=25000
 11 16787         CENARGEN        CLONEEND
 12 15150         UOKNOR          SHOTGUN
 13 10651         TIGR_JCVIJTC    CLONEEND
 14 151           UOKNOR          FINISHING
 15 49            WUGSC           CLONEEND
    36809945      total

 1  527017        BCCAGSC         EST
 2  207204        MARC            EST
 3  171667        MARC            PCR
 4  81913         BARC            EST
 5  18623         SC              EST 
 6  2485          UIACBCB         EST
    1019449       total

STRATEGY & TRACE_TYPE_CODE counts

 COUNT           CENTER_NAME     STRATEGY        TRACE_TYPE_CODE
 12545304        BCM             .               WGS
 11425910        BCM             WGA             WGS
 5223683         BCM             CLONE           SHOTGUN
 4479883         BCM             POOLCLONE       SHOTGUN
 1044963         BCM             .               SHOTGUN
 892385          BCM             SNP             WGS
 737900          NISC            CLONE           SHOTGUN
 125597          BCCAGSC         CLONEEND        CLONEEND
 114753          UIUC            CLONEEND        CLONEEND 
 65171           TIGR            CLONEEND        CLONEEND
 53556           GSC             CLONEEND        CLONEEND
 26246           CENARGEN        .               WGS
 25454           BARC            .               CLONEEND
 16892           BCM             CLONEEND        CLONEEND
 16787           CENARGEN        CLONEEND        CLONEEND
 12195           UOKNOR          .               SHOTGUN
 10651           TIGR_JCVIJTC    CLONEEND        CLONEEND
 2955            UOKNOR          CLONE           SHOTGUN
 151             UOKNOR          .               FINISHING
 49              WUGSC           CLONEEND        CLONEEND

 527017          BCCAGSC         EST             EST
 145820          MARC            EST             EST
 117958          MARC            COMPARATIVE     PCR
 81913           BARC            EST             EST
 61384           MARC            CLONE           EST
 53709           MARC            Re-Sequencing   PCR
 18623           SC              EST             EST
 2485            UIACBCB         .               EST

3' VECTOR TRIMMED counts

 CENTER_NAME     TRACE_TYPE_CODE TOTAL           3'CLV<LEN   QUAL==0          UMD.FRG
 BCM             WGS             24863599        10968979    551114           24050767
 BCM             SHOTGUN         10748529        5052692     23419            10068499
 NISC            SHOTGUN         737900          28972       0                735488
 BCCAGSC         CLONEEND        125597          125484      8926             113790
 UIUC            CLONEEND        114753          90243       0                106247
 TIGR            CLONEEND        65171           46389       0                64903
 GSC             CLONEEND        53556           53556       53556 (all)      0           !!! all have 0 quals and were excluded
 CENARGEN        WGS             26246           26246       0                25976
 BARC            CLONEEND        25454           25454       0                25387
 BCM             CLONEEND        16892           6751        0                16863
 CENARGEN        CLONEEND        16787           16787       0                16628
 UOKNOR          SHOTGUN         15150           2885        12195            0
 TIGR_JCVIJTC    CLONEEND        10651           339         0                10644
 UOKNOR          FINISHING       151             0           151              151
 WUGSC           CLONEEND        49              0           0                0

 BCCAGSC         EST             527017          524173      772              0
 MARC            EST             207204          207204      0                0
 MARC            PCR             171667          171667      0                0
 BARC            EST             81913           78597       0                0
 SC              EST             18623           7350        0                0
 UIACBCB         EST             2485            2485        0                0

ZERO QUALITY COUNTS

Counts

 CENTER_NAME     TRACE_TYPE_CODE  COUNT
 BCM             WGS              551114
 GSC             CLONEEND         53556
 BCM             SHOTGUN          23419
 UOKNOR          SHOTGUN          12195
 BCCAGSC         CLONEEND         8926
 BCCAGSC         EST              772
 UOKNOR          FINISHING        151
 TOTAL                            650134

For 0 quality reads, assign quality 20 to bases 1..700, 0 to bases 701..
Volumes 026..039 have been fixed

Local Data

Files & Dirs

 /fs/szasmg3/bos_taurus/data/
 /fs/szasmg2/Drosophila/D_pseudoobscura/Vectors
 /nfshomes/dpuiu/db/UniVec

Software

Figaro

trims vector only at 5' end
call lucy trimming for qualities

Lucy

both vector sequence and splice sites are required

Atlas

web site
atlas-screen-trim-file : "calls cross_match and atlas-screen-window to create trimmed reads file (scan in from each end of read looking for 50-base windows of high quality and no vector); "

Contaminant search

nucmer reads CLIPPING range to UniVec & EcoliK12

UniVec

Ref

                 #seqs   min     max     mean    median  n50     sum
 UniVec          2861    12      48551   231     99      781     660,151
 UniVec_Core     1348    12      48551   243     98      967     327,641

Hits: alignment length

 bp      #reads  min     max     mean    median  n50     sum
 19      4548466 19      1045    28.37   23      27      129025025
 20      3684852 20      1045    30.56   25      28      112616359
 30      1097357 30      1045    48.04   38      43      52714583
 40      484661  40      1045    66.36   47      53      32163896
 100     54334   100     1045    198     116     223     10772815        # many are ESTs

Ecoli

Ref:

 K12 4,639,675 bp

Hits: alignment length

 bp      #reads  min     max     mean    median  n50     sum
 19      275109  19      1223    30.66   19      20      8435470
 20      102550  20      1223    50.29   21      161     5156849
 30      19032   30      1223    178     37      706     3381214
 40      9234    40      1223    329     171     738     3034293
 100     6781    100     1223    424     223     749     2876432
 200     4378    200     1223    575     696     771     2516916

BCM vectors

                 #seqs   min     max     mean    median  n50     sum
 BCM             14      2580    33180   9379    5821    32705   131312

Vector/Splice site search

Strategy

1. Select all the reads in the same volume that belong to one particular library; same CENTER_NAME, STRATEGY & TRACE_TYPE_CODE
2. Get the quality clipping time: CLIP_QUALITY_LEFT & CLIP_QUALITY_RIGHT
3. Separate reads in 2 sets according to direction TRACE_END: FORWARD & REVERSE
4. Get the most frequent kmers in each set (24 & 8 bp)
5. Check if the most frequent kmers are overrepresented
6. Check if the most frequent 8mers are present in the most frequent 24mers
7. Try to extend the 24mers by a few bp => linkers
8. Align linkers to the opposite stand sequences using nucmer
9. Extract the subsequences adjacent(following) to linker (50..150bp)
10. Align the subsequences; if they align we've probably identified the vector
11. Identify the vector name/id by alignment to UniVec => several alignments
12. Check if the forward/reverse vector(s) are the same : we should find a common vector sequence; the UniVec alignments should be adjacent
13. create the Lucy vector & splice files; the splice contains the linker+vector
14. run lucy & trim input reads according to Lucy clr
15. align lucy trimmed reads to linker,vector,splice & UniVec.dust
16. align input reads to linker,vector,splice & UniVec.dust
17. compare the 15. & 16. counts

Example

1. volume 011 : 500,000 reads CENTER_NAME=BCM, TRACE_TYPE_CODE=WGS
2.
3. 249,611 TRACE_END=F & 250,389 TRACE_END=R
4. kmers: 8 8bp most frequent kmers are shared by the FORWARD & REVERSE strands ; no 24bp kmers are shared

 ==> 24.fwd/kmers.tab <==
 AGTTCGACTGCAAGTAGTTCATCA      TGATGAACTACTTGCAGTCGAACT        2463 # contains AGTAGTTC
 GAGTTCGACTGCAAGTAGTTCATC      GATGAACTACTTGCAGTCGAACTC        2189
 CGAGTTCGACTGCAAGTAGTTCAT      ATGAACTACTTGCAGTCGAACTCG        1996
 TCGAGTTCGACTGCAAGTAGTTCA      TGAACTACTTGCAGTCGAACTCGA        1593
 GTTCGACTGCAAGTAGTTCATCAA      TTGATGAACTACTTGCAGTCGAAC        1023
 GAGTTCGACTGCAGTAGTTCATCA      TGATGAACTACTGCAGTCGAACTC        812
 CGAGTTCGACTGCAGTAGTTCATC      GATGAACTACTGCAGTCGAACTCG        777
 GTTCGACTGCAAGTAGTTCATCAT      ATGATGAACTACTTGCAGTCGAAC        769
 TCGAGTTCGACTGCAGTAGTTCAT      ATGAACTACTGCAGTCGAACTCGA        637
 ATCGAGTTCGACTGCAAGTAGTTC      GAACTACTTGCAGTCGAACTCGAT        594
 
 ==> 08.fwd/kmers.tab <==
 AGTAGTTC      GAACTACT        86477
 CAGTAGTT      AACTACTG        67681
 AGTTCTCA      TGAGAACT        61556
 TAGTTCTC      GAGAACTA        60964
 GTAGTTCT      AGAACTAC        57866
 AGTTCATC      GATGAACT        49676
 TAGTTCAT      ATGAACTA        45298
 GTTCATCA      TGATGAAC        42117
 GCAGTAGT      ACTACTGC        41391
 GTAGTTCA      TGAACTAC        40694
 
 ==> 24.rev/kmers.tab <==
 TATCGATGGTACAGTAGTTCATCA      TGATGAACTACTGTACCATCGATA        999 # contains AGTAGTTC
 CTATCGATGGTACAGTAGTTCATC      GATGAACTACTGTACCATCGATAG        774
 GCTATCGATGGTACAGTAGTTCAT      ATGAACTACTGTACCATCGATAGC        600
 CGCTATCGATGGTACAGTAGTTCA      TGAACTACTGTACCATCGATAGCG        432
 ATCGATGGTACAGTAGTTCATCAT      ATGATGAACTACTGTACCATCGAT        417
 ATCGATGGTACAGTAGTTCATCAA      TTGATGAACTACTGTACCATCGAT        380
 ATCAGATGGTACAGTAGTTCATCA      TGATGAACTACTGTACCATCTGAT        373
 ATCGATGGTACAGTAGTTCATCAC      GTGATGAACTACTGTACCATCGAT        265
 CTATCGATGGTAAGTAGTTCATCA      TGATGAACTACTTACCATCGATAG        235
 TCAGATGGTACAGTAGTTCATCAA      TTGATGAACTACTGTACCATCTGA        224
 
 ==> 08.rev/kmers.tab <==
 AGTTCATC      GATGAACT        85127
 TAGTTCAT      ATGAACTA        77902
 GTTCATCA      TGATGAAC        75585
 TAGTTCTC      GAGAACTA        68057
 AGTTCTCA      TGAGAACT        67277
 GTAGTTCT      AGAACTAC        64894
 GTAGTTCA      TGAACTAC        62607
 CGTAGTTC      GAACTACG        52031
 AGTAGTTC      GAACTACT        51013
 ACGTAGTT      AACTACGT        31552

7. Get linker sequences

 >linker.fwd 27bp
 TCGAGTTCGACTGCAAGTAGTTCATCA
 >linker.rev 27bp
 CTAATCAGATGGTACAGTAGTTCATCA 
  
 #>linker.rev 40 bp Art's  (13 more bp at 5')        
 #TATGACCATGCGCCTAATCAGATGGTACAGTAGTTCATCA

 #GCTATCGATGGTACAGTAGTTCATCAT is the most frequent rev seq 27 kmers but not the linker (few snp differences)

8 & 9 Align reads to linkers using nucmer

Fwd:

 nucmer -l 12 -c 24 -r linker.fwd.seq ../bos_taurus.$v.r.fasta 
 #  nucmer -l 12 -c 24 -r kmers.seq ../bos_taurus.$v.r.fasta  
 show-coords out.delta | awk '{print $19,$5,$13}' > ! out.clr
 extractfromfastanames.pl -clr -f out.clr < ../bos_taurus.$v.r.fasta >! out.seq

Rev:

 nucmer -l 12 -c 24 -r linker.rev.seq ../bos_taurus.$v.f.fasta
 #  nucmer -l 12 -c 24 -r kmers.seq ../bos_taurus.$v.f.fasta  
 show-coords out.delta | awk '{print $19,$5,$13}' > ! out.clr
 extractfromfastanames.pl -clr -f out.clr < ../bos_taurus.$v.f.fasta >! out.seq

Both:

 clrFasta out.seq >! out.cseq
 fasta2tab.pl out.cseq | sort -k2 > ! out.tab
 nucmer -c 40 out.cseq ~/db/UniVec -p vector
 delta-filter -q vector.delta >! vector.filter-q.delta
 show-coords vector.filter-q.delta | sort -n | head

 cat vector.filter-q.delta | grep "^>" | count.pl -c 1 -m 2

10. Extract "vector reads"

 >399553028  # 24.fwd     
 TGATGAACTACTGTACCATCTGATTAGGCGCATGGTCATAGCTGTTTCCTGTGTGAAATT
 GCTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGG
 GTGTCAAATGAGAGACCTAACTCACATTCAACTTTTTTTTTTTTTCTGCCCTCTATTCTA
 ...
 >400269118 #24.rev
 TGATGAACTACTTGCAGTCGAAATCGAATCATCACTGGCCGTCCTTTTACAACGTCGTGA
 CTGGGAAAACCCTGGCGTTACCCAACTTAATCCGCCTTGCAGCACATCCCCCTTTCCCCC
 AGCTGGCGTAAAAACGTAAAAAGCCCCGCACCGATCGCCCTTTCCCAACAGGTTGCCCAG

11. Align "vector reads" to UniVec

 show-coords 24.fwd/400269118-UniVec.delta 24.rev/399553028-UniVec.delta | grep J01636.1
     31  148  | 1175 1292  | 118   118  |  95.76  |     1276     7477  |     9.25     1.58  | 399553028.rev gnl|uv|J01636.1:1-7477
     32  199  | 1302 1463  | 168   162  |  90.48  |      653     7477  |    25.73     2.17  | 400269118     gnl|uv|J01636.1:1-7477

12. 10bp distance between the 2 alignments
13. Lucy files

 $ more vector.seq
   >J01636 E.coli lactose operon with lacI, lacZ, lacY and lacA genes
   GACACCATCGAATGGCGCAAAACCTTTCGCGGTATGGCATGATAGCGCCCGGAAGAGAGTCAATTCAGGG
   TGGTGAATGTGAAACCAGTAACGTTATACGATGTCGCAGAGTATGCCGGTGTCTCTTATCAGACCGTTTC
   CCGCGTGGTGAACCAGGCCAGCCACGTTTCTGCGAAAACGCGGGAAAAAGTGGAAGCGGCGATGGCGGAG
   CTGAATTACATTCCCAACCGCGTGGCACAACAACTGGCGGGCAAACAGTCGTTGCTGATTGGCGTTGCCA
   ...
 
 $ more splice.seq
   >J01636.for.begin vector+linker.rev
   TGAATGTGAGTTAGGTCTCTCATTTGACACCCCAGGCTTTACACTTTATGCTTCCGGCTC
   GTATGTTGTGTGGAATTGTGAGCGGATAGCAATTTCACACAGGAAACAGCTATGACCATG
   CGCCTAATCAGATGGTACAGTAGTTCATCA
   >J01636.for.end  rev(linker.fwd)+vector 
   TGATGAACTACTTGCAGTCGAAATCGAATCATCACTGGCCGTCCTTTTACAACGTCGTGA
   CTGGGAAAACCCTGGCGTTACCCAACTTAATCCGCCTTGCAGCACATCCCCCTTTCCCCC
   AGCTGGCGTAAAAACGTAAAAAGCCCCGCA
   >J01636.rev.begin (revcomp of J01636.for.end)
   TGCGGGGCTTTTTACGTTTTTACGCCAGCTGGGGGAAAGGGGGATGTGCTGCAAGGCGGA
   TTAAGTTGGGTAACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAAGGACGGCCAGTGAT
   GATTCGATTTCGACTGCAAGTAGTTCATCA
   >J01636.rev.end (revcomp of J01636.for.begin)
   TGATGAACTACTGTACCATCTGATTAGGCGCATGGTCATAGCTGTTTCCTGTGTGAAATT
   GCTATCCGCTCACAATTCCACACAACATACGAGCCGGAAGCATAAAGTGTAAAGCCTGGG
   GTGTCAAATGAGAGACCTAACTCACATTCA

 # splice=linker+vector  
      3      120  |     1175     1292  |      118      118  |    95.76  |      150     7477  |    78.67     1.58  | J01636.for.begin   J01636
     32      131  |     1302     1399  |      100       98  |    96.00  |      150     7477  |    66.67     1.31  | J01636.for.end     J01636

14. Run lucy & trim reads

 $ /nfshomes/dpuiu/szdevel/SourceForge/lucy-1.19p/lucy \ 
     -v vector.seq splice.seq
     -o bos_taurus.lucy.seq bos_taurus.lucy.qual \
     -debug  bos_taurus.lucy.info \
     bos_taurus.seq bos_taurus.qual

 # Trim clr
 $ clrFasta bos_taurus.seq > bos_taurus.cseq

15. Align lucy output to linker, vector, splice & UniVec.dust

 $ nucmer -l 12 -c 24 ~/db/vector.seq  bos_taurus.lucy.cseq -p vector-bos_taurus.lucy
 $ nucmer -l 16 -c 30 ~/db/vector.seq  bos_taurus.lucy.cseq -p vector-bos_taurus.lucy
 $ nucmer -l 16 -c 30 ~/db/splice.seq  bos_taurus.lucy.cseq -p splice-bos_taurus.lucy
 $ nucmer -l 16 -c 30 ~/db/UniVec.dust bos_taurus.lucy.cseq -p UniVec.dust-bos_taurus.lucy

16. Align input to linker, vector, splice & UniVec.dust

 $ nucmer -l 12 -c 24 ~/db/linker.seq bos_taurus.seq -p linker-bos_taurus
 $ nucmer -l 16 -c 30 ~/db/vector.seq bos_taurus.seq -p vector-bos_taurus
 $ nucmer -l 16 -c 30 ~/db/splice.seq bos_taurus.seq -p splice-bos_taurus
 $ nucmer -l 16 -c 30 ~/db/UniVec.dust bos_taurus.seq -p UniVec.dust-bos_taurus

Libraries

Count how many reads got trimmed

 infoseq *seq | getSummary.pl -c 1 -t original.LEN
 
 cat bos_taurus.lucy.info | awk '{print $4-$3}' | getSummary.pl -t lucy.CLR >! bos_taurus.lucy.summary  
 cat bos_taurus.lucy.info | getSummary.pl -c 14 -t lucy.CLV5 -nh >> bos_taurus.lucy.summary
 cat bos_taurus.lucy.info | getSummary.pl -c 15 -t lucy.CLV3 -nh >> bos_taurus.lucy.summary

011.BCM.WGS FORWARD

vector: J01636
UniVec: gnl|uv|J01636.1:1-7477 E.coli lactose operon with lacI, lacZ, lacY and lacA genes

 ll ~dpuiu/db/J01636*
 -rw-rw-r--  1 dpuiu dpuiu 7651 Jan  9 15:56 /nfshomes/dpuiu/db/J01636
 -rw-rw-r--  1 dpuiu dpuiu  105 Jan 14 07:17 /nfshomes/dpuiu/db/J01636linker
 -rw-rw-r--  1 dpuiu dpuiu  840 Jan 13 13:43 /nfshomes/dpuiu/db/J01636splice

 cat  ~dpuiu/db/J01636* | infoseq
 J01636            7477   53.43
 J01636.linker.fwd 27     44.44
 J01636.linker.rev 27     37.04
 J01636.for.begin  150    44.67
 J01636.for.end    150    51.33
 J01636.rev.begin  150    51.33
 J01636.rev.end    150    44.67

249,611 reads:
91% got vector trimmed at the 5'
0.4% (1149) got vector trimmed at the 3'

                 #elem   #0s     min     max     mean    median  n50     sum
 original.LEN    249611  0       437     2349    1082    991     1009    270035781     
 lucy.CLV5       249611  21215   0       741     25.03   25      27      6247415
 lucy.CLV3       249611  248462  0       1047    3.49    0       859     870344

Original reads hit counts:

10975 linker.fwd
133   linker.rev
166   splice
152   vector
228   UniVec.dust

Lucy trimmed read counts

2 linker.fwd
0 linker.rev
1 splice
1 vector
6 UniVec.dust (only 3 are >40bp)

011.BCM.WGS REVERSE

                 #elem   #0s     min     max     mean    median  n50     sum
 original.LEN    250389  0       502     2148    1085    993     1012    271691094
 lucy.CLR        250389  7345    0       1281    795     876     892     198982171
 lucy.CLV5       250389  20271   0       668     26.52   27      29      6641362
 lucy.CLV3       250389  249269  0       997     3.35    0       861     839029

Original reads hit counts:

 linker.fwd      113
 linker.rev      3812
 splice          143
 UniVec.dust     237
 vector          4318

Lucy trimmed reads hit counts:

 linker.fwd      1
 linker.rev      0
 splice          1
 UniVec.dust     10
 vector          1

030.BCM.SHOTGUN

same linker/vector/splice as BCM.WGS
2.5% (4K out of 160K) reads contain linker & vector at 3'

                 #elem   #0s     min     max     mean    median  n50     sum
 original.LEN    8411    0       325     1685    1181    1240    1314    9933150
 lucy.CLR        8411    8       0       1054    841     863     874     7070994
 lucy.CLV5       8411    568     0       232     27.01   28      29      227206
 lucy.CLV3       8411    2325    0       1040    597     794     851     5023445

Original reads hit counts:

 linker.fwd      4314
 linker.rev      4125
 splice          7816
 UniVec.dust     4212
 vector          6750
 vector          27235

Lucy trimmed reads hit counts:

 linker.fwd      3
 linker.rev      1
 splice          1
 UniVec.dust     13
 vector          0

001.NISC

Vector: pOTW13
UniVec: 3 partial seqs

 gnl|uv|NGB00080.1:1-198 pOTW13 with linkers
 gnl|uv|NGB00080.1:718-888 pOTW13 with linkers
 gnl|uv|NGB00080.1:1490-1654-49 pOTW13 with linkers

 ll /nfshomes/dpuiu/db/NGB00080*
 -rw-rw-r--  1 dpuiu dpuiu 1083 Jan 14 20:43 /nfshomes/dpuiu/db/NGB00080
 -rw-r--r--  1 dpuiu dpuiu   94 Jan 14 21:01 /nfshomes/dpuiu/db/NGB00080linker
 -rw-r--r--  1 dpuiu dpuiu 2183 Jan 14 20:44 /nfshomes/dpuiu/db/NGB00080splice

 cat  /nfshomes/dpuiu/db/NGB00080* | infoseq
 NGB00080       1054   50.00
 NGB00080.linker.fwd 24     45.83
 NGB00080.linker.rev 26     53.85
 NGB00080.for.beg 518    46.14
 NGB00080.for.end 518    50.48
 NGB00080.rev.begin 518    50.48
 NGB00080.rev.beg 518    46.14

944 read sample

                 #elem   #0s     min     max     mean    median  n50     sum
 original.LEN    944     0       652     1017    735     721     722     693668
 lucy.CLR        944     39      0       886     415     422     522     391333
 lucy.CLV5       944     121     0       275     34.05   33      35      32143
 lucy.CLV3       944     18      0       885     410     409     511     387007

Original reads hit counts:

 linker.fwd      479
 linker.rev      492
 splice          910
 UniVec.dust     0
 vector          939

Lucy trimmed reads hit counts:

 linker.fwd      1
 linker.rev      0
 splice          0
 UniVec.dust     9
 vector          1

060.BCCAGSC.CLONEEND

Linkers:

 linker.fwd CCCTGCTTTGTCTGGAAGGGGTTCCCGACCT
 linker.rev CAGGAGGGGAGAAAGGGCTCAGAGG

No common vector !!!

 wc -l *clb
   60746 bos_taurus.060.f.clb  #18 reads original align to UniVec (nucmer default params)
   60836 bos_taurus.060.r.clb
 
 Fwd:
    329      428  |      440      535  |      100       96  |    91.00  |      503     1585  |    19.88     6.06  | 723951410  gnl|uv|U30497.1:3230-4814 Cloning vector pAS2-1
    330      370  |       89       49  |       41       41  |   100.00  |      503      143  |     8.15    28.67  | 723951410  gnl|uv|U67875.1:6541-6683 pESP-I yeast expression vector
    330      370  |       94       54  |       41       41  |   100.00  |      503      143  |     8.15    28.67  | 723951410  gnl|uv|U67875.1:6541-6683 pESP-I yeast expression vector
 
  Rev:
      1       96  |       71      165  |       96       95  |    93.81  |      203      165  |    47.29    57.58  | 724018013  gnl|uv|AF133437.1:16659-16823 Cloning vector pCYPAC6
     50      143  |        1       94  |       94       94  |    92.71  |      203       94  |    46.31   100.00  | 724018013  gnl|uv|U80929.2:2858-2951     Cloning vector pBACe3.6

017.UIUC.CLONEEND

No overrepresented kmers

 wc -l *clb
  17978 bos_taurus.017.f.clb
  17911 bos_taurus.017.r.clb
 
 ==> 24.fwd/kmers.tab <==
 CCCTGCTTTGTCTGGAAGGGGTTC        GAACCCCTTCCAGACAAAGCAGGG        9
 CTGCTTTGTCTGGAAGGGGTTCCC        GGGAACCCCTTCCAGACAAAGCAG        9
 
 ==> 24.rev/kmers.tab <==
 GAATGTTGAGCTTTAGCCAACTTT        AAAGTTGGCTAAAGCTCAACATTC        4
 TCTGAATGTTGAGCTTTAGCCAAC        GTTGGCTAAAGCTCAACATTCAGA        4
 
 ==> 8.fwd/kmers.tab <==
 TTTTTTTT        AAAAAAAA        55
 AAGGGGTT        AACCCCTT        35
 
 ==> 8.rev/kmers.tab <==
 GTCTGGAA        TTCCAGAC        41
 TCTGGAAG        CTTCCAGA        39

No UniVec hits

010.TIGR.CLONEEND

No overrepresented kmers

 wc -l *clb
 5479 bos_taurus.032.f.clb
 5174 bos_taurus.032.r.clb
 
 ==> 24.fwd/kmers.tab <==
 CTTGTGTTGGCCCAGGCAAGTCCA        TGGACTTGCCTGGGCCAACACAAG        30
 TTGTGTTGGCCCAGGCAAGTCCAA        TTGGACTTGCCTGGGCCAACACAA        30
 
 ==> 24.rev/kmers.tab <==
 CTGCCTCTTGTGTTGGCCCAGGCA        TGCCTGGGCCAACACAAGAGGCAG        16
 GCTGCCTCTTGTGTTGGCCCAGGC        GCCTGGGCCAACACAAGAGGCAGC        15
 
 ==> 8.fwd/kmers.tab <==
 GAGTGGGT        ACCCACTC        176
 GGAGTGGG        CCCACTCC        171
 
 ==> 8.rev/kmers.tab <==
 TGGAGTGG        CCACTCCA        182
 GGAGTGGG        CCCACTCC        181

No UniVec hits

...

070.BCM.CLONEEND

No frequent kmers

 wc -l *clb
   6027 bos_taurus.070.f.clb
   6236 bos_taurus.070.r.clb
 
 ==> 24.fwd/kmers.tab <==
 GGACTCTCAGAGTCTTCTCCAACA        TGTTGGAGAAGACTCTGAGAGTCC        18
 ACTGGTTGGATCTCCTTGCAGTCC        GGACTGCAAGGAGATCCAACCAGT        18

 ==> 24.rev/kmers.tab <==
 ATAAAATCTGAGCCACCAGGGAAG        CTTCCCTGGTGGCTCAGATTTTAT        1
 CTATTGGTTCATATGGTCAACGTC        GACGTTGACCATATGAACCAATAG        1
 
 ==> 8.fwd/kmers.tab <==
 TTTTTTTT        AAAAAAAA        86
 CTTCTCCA        TGGAGAAG        75
 
 ==> 8.rev/kmers.tab <==
 TATAGTGT        ACACTATA        9
 ATATAGGG        CCCTATAT        8

No alignments to BCM WGS vector

Bos taurus redo

Contents

BCM

NCBI Data

CENTER_NAME counts

TRACE_TYPE_CODE counts

STRATEGY & TRACE_TYPE_CODE counts

3' VECTOR TRIMMED counts

ZERO QUALITY COUNTS

Local Data

Files & Dirs

Software

Contaminant search

UniVec

Ecoli

BCM vectors

Vector/Splice site search

Strategy

Example

Libraries

011.BCM.WGS FORWARD

011.BCM.WGS REVERSE

030.BCM.SHOTGUN

001.NISC

060.BCCAGSC.CLONEEND

017.UIUC.CLONEEND

010.TIGR.CLONEEND

...

070.BCM.CLONEEND

Navigation menu

Bos taurus redo

BCM

NCBI Data

CENTER_NAME counts

TRACE_TYPE_CODE counts

STRATEGY & TRACE_TYPE_CODE counts

3' VECTOR TRIMMED counts

ZERO QUALITY COUNTS

Local Data

Files & Dirs

Software

Contaminant search

UniVec

Ecoli

BCM vectors

Vector/Splice site search

Strategy

Example

Libraries

011.BCM.WGS FORWARD

011.BCM.WGS REVERSE

030.BCM.SHOTGUN

001.NISC

060.BCCAGSC.CLONEEND

017.UIUC.CLONEEND

010.TIGR.CLONEEND

...

070.BCM.CLONEEND

Navigation menu

Search