Pine tree

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Links

Data

UCDAVIS plone

  • Links
 https://dendrome.ucdavis.edu/TGPlone/research-projects/pinerefseq  
 dpuiu
 ddr5fft6 
 https://dendrome.ucdavis.edu/TGPlone/research-projects/pinerefseq/files/library-and-flow-cell-data/prs-tracking-database-archive/

IPST ftp

 ftp genomepc1.umd.edu
 ftpuser
 pinegenome

 cd PineUpload052911/
 bin
 prompt             # no Y/N?
 mget *

Local data

 ginkgo:
 /fs/szattic-asmg7/PINE/PineUpload052911
 /fs/szattic-asmg7/PINE/PineUpload070711

PineUpload052911

Chloroplast

                len      gc%
 cChloroplast   120481   38.55

cBACs

 .       elem       min    q1     q2     q3     max        mean       n50        sum            
 len     102        8288   89909  116121 140549 172161     113400     126689     11566806       
 gc%     102        34.44  36.56  37.61  38.80  52.88      37.94      37.66      3870.87        

Reads

 lane           readLen   #mates        mea,std      ~gc%
 FC638TR_001_8  146       22,729,231    400           39.04
 FC638TR_002_8  146       18,412,638    400           39.04
  • Quality decreases sharply after pos 120
 FC638TR.qual.png
  • First 10bp of each read have higher AG count
 FC638TR.content.png
  • Over 0.5% Ns certain positions
 fwd: 1.015% pos=100 ; 0.81% pos=119
 rev: 1.114% pos=101 ; 0.92% pos=107 ; 0.87% pos=30; 0.21% pos 21
 FC638TR.Ns.png
  • GC% variation: cBAC(37.5%) < cChloroplast(38.5%) < reads(39%) < mito (44%+)
  • cCholoplast alignments (bwasw)
 lane                  #hits   %hits  #hits(uniq) 
 FC638TR_001_8_1	475254	2.09   468309
 FC638TR_001_8_2	473331	2.08   466185
 FC638TR_002_8_1	1009331	5.48   995291
 FC638TR_002_8_2	1004341	5.45   990122


  • cBAC alignments (bwasw)
 lane                  #hits   %hits   #hits(uniq) 
 FC638TR_001_8_1	9722204	42.77   9533849
 FC638TR_001_8_2	9481188	41.71   9303475
 FC638TR_002_8_1	7684164	41.73   7535809
 FC638TR_002_8_2	7469151	40.56   7330078

Sampled reads

  • 100K sampled reads from each library (2*2*100K=400K)
 .       elem       min    q1     q2     q3     max        mean       n50        sum            
 gc%     400000     0.68   34.93  39.04  43.15  95.89      39.20      40.41      .
  • FC638TR_001_8_1 alignments
 ref            qry               aligner      #hits      %hits   %identity(median)
 cBAC           FC638TR_001_8_1   bwasw        42971      43 
                                  nucmer       12477      12.5    95
                                  bowtie       1186       1.2%
 cChloroplast                     bwasw        2031       2%
                                  nucmer       1943       1.9%    100
                                  bowtie       1490       1.5%
  • FC638TR_00[12]_8_[12] bwa alignments
 ref            qry               aligner      #hits      %hits 
 cBAC           FC638TR_001_8_1   bwasw        42971      43
                FC638TR_001_8_2                41915      42
                FC638TR_002_8_1                42128      42
                FC638TR_002_8_2                40606      41

 cChloroplast   FC638TR_001_8_1                2031       2
                FC638TR_001_8_2                2033       2
                FC638TR_002_8_1                5370       5.3
                FC638TR_002_8_2                5330       5.3

SOAPdenovo's

 #scaffold stats
 .                                     elem       min    q1     q2     q3     max        mean       n50        sum
 -K47           -max_rd_len100         211820     100    143    156*   187    23273      227.95     .          48284629

 -K31           -max_rd_len100         13747338   100    100    100    100    9185       108.04     .          1485269562
 -K31 -d2  -D3  -max_rd_len100         74820      100    105    125    390    31673      320.75     .          23998536  
 -K31 -d20 -M3  -max_rd_len100         7859*      100    113    139    284    43079*     331.49     .          2605184*            

 -K27 -d 2 -D 3 -max_rd_len100         70246      100    107    137    413    30683      369.81     .          25977758
 -K27 -d 2 -D 2 -max_rd_len146         224963     100    110    128    343    23410      260.64     .          58635190

SOAPdenovo-31mer -K 27 -d 2 -D 3 -max_rd_len 100

 #scaffold stats
 .                          elem   min    q1     q2     q3     max    mean     n50    sum
 scf                        70246  100    107    137    413    30683* 369.81   .      25977758
 ctg                        8641885 28    28     31     37     7238   36.1     .      312425669

Alignment1

 nucmer default parameters 
 # Legend:
 all                        : all SOAPdenovo scaffolds
 cBAC                       : scaffolds aligned to cBACs
 cChloroplast               : scaffolds aligned to cChloroplast
 mito                       : scaffolds aligned to at least one of the 31 complete plant mitochondrion sequence
 mito.Cycas_taitungensis    : scaffolds aligned to at least one of the Cycas_taitungensis mitochondrion sequence (most hits)
 other                      : unaligned scaffolds
 # scaffold length stats
 .                          elem   min    q1     q2     q3     max    mean     n50    sum
 all                        70246  100    107    137    413    30683  369.81   .      25977758
 cBAC                       1839   100    124    242    625    23267  637.13   .      1171678
 cChloroplast               73     100    117    139    185    416    161.47   .      11787        # why so bad???
 mito                       68     131    867    2274   7241   30683  4675.18  .      317912
 mito.Cycas_taitungensis    64     111    844    1931   7114   30683* 4529.91  .      289914
 other                      68266  100    106    136    412    26715  358.54   .      24476381
 #scaffold gc stats
 .                          elem   min    q1     q2     q3     max    mean     n50    sum
 all                        70246  4.90   35.40  40.74  44.52  74.26  39.78    .      .
 cBAC                       1839   10.64  35.63  41.22  44.87  74.26  39.95    .      .
 cChloroplast               73     25.65  31.09  33.33  36.89  42.31  33.76    .      .
 mito                       68     43.08  45.96  47.45  49.19  56.41  47.77    .      .
 mito.Cycas_taitungensis    64     41.44  46.27  47.81  50.00  56.41  48.16    .      .
 other                      68266  4.90   35.40  40.71  44.50  70.00  39.77    .      .
  • The longest assembled scaffold was 30683bp and aligned to the mitochondrion database.
  • The mitochondrion gc% seems to be significantly higher than the one of rest of the genome (48% vs 40%)
  • The Cycas taitungensis mitochondrion (414903bp, 46.92%gc) had the most scaffolds aligned to it (64 out of 68).
 NC_009618	Cycas taitungensis chloroplast, complete genome    DNA; circular; Length: 163,403 nt
 NC_010303	Cycas taitungensis mitochondrion, complete genome  DNA; circular; Length: 414,903 nt
 Cycas_taitungensis_mito-chloroplast.png
  • Mitochondrial scaffolds
 .                    elem       min    q1     q2     q3     max        mean       n50        sum           
 scf                  68         131    867    2274   7241   30683      4675.18    9407       317912          # used for alignment
 scf.gc%              68         43.08  45.96  47.45  49.19  56.41      47.77      47.45      3248.1 
 scf.noGaps           68         131    743    2049   6660   27931      4262.46    9052       289847         
  • Reads aligned to mitochondrial scaffolds (bwa bwasw)
 lane               #hits  %hits
 FC638TR_001_8_1    12307  0.054
 FC638TR_001_8_2    11933 
 FC638TR_002_8_1    28707  0.12
 FC638TR_002_8_2    27211
 total              80158          # 20X cvg for 100bp read len & 400K mito genome ; 29X  cvg for 146bp read len

Alignment2

 nucmer -l 20 -c 20; delta-filter -l 65 -q -o 75 ; filter for gc% >=44
 #some of the mito hits align to cChloroplast & cBAC => might have an overestimate
 # Mitochondrial scaffolds
 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 scf.len              102        101    608    1931   7271   30683      5044.88    11204      514578          
 scf.gc%              102        44.07  46.12  47.45  49.33  56.41      48.05      47.47      4901.06
 lane               #hits  %hits
 FC638TR_001_8_1    18614
 FC638TR_001_8_2    18035
 FC638TR_002_8_1    43961
 FC638TR_002_8_2    42101
 total              122707            # 30X cvg for 100bp read len & 400K mito genome

Alignments3

 nucmer -l 20 -c 20; delta-filter -l 100 -q -o 75
 .               elem   min  q1   q2    q3    max    mean     n50  sum
 cChloroplast    136    100  117  142   187   628    168.34   0    22894
 cBAC            6385   100  116  187   499   23267  597.00   0    3811871
 mito            84     110  479  1791  7050  30683  4268.99  0    358595
 other           63641  100  106  134   409   22471  342.30   0    21784398

SOAPdenovo-31mer -K 31 -d 20 -M 3 -max_rd_len 100

 #scaffold stats
 .                          elem   min    q1     q2     q3     max    mean     n50    sum
 scf                        7859*  100    113    139    284    43079* 331.49   .      2605184
 ctg                        200062 32     33     37     47     10392  48.52    .      9707307
# scaffold length stats
 .                          elem   min    q1     q2     q3     max    mean     n50    sum
 all                        7859*  100    113    139    284    43079* 331.49   .      2605184
 cChloroplast               20     111    193    436    6140   43079  5951.05  0      119021
 cBAC                       5117   100    114    141    320    13733  334.94   0      1713870
 mito                       8      101    134    685    1396   2166   749.75   0      5998        !!! VERY BAD
 other                      2714   100    111    133    226    7353   282.35   0      766295

SOAPdenovo-31mer -K 31 -d 48 -max_rd_len 100 -M 3 choloplast_mated_reads

 #scaffold stats
 .                    elem       min    q1     q2     q3     max        mean       n50        sum            
 scf                  20         111    193    436    6140   42707      5928.20    0          118564

PineUpload070711

Ecoli

                len     gc%
 cE_coli        4639675 50.79  

Cloning vector

                len    gc% 
 pFosDT5_2      8345   47.93

Drosophila refseq

 Chromosome      len            gc%
 2L              23,011,544     41
 2R              21,146,708     43
 3L              24,543,557     41
 3R              27,905,053     42
 4               1,351,857      35
 X               22,422,827     42 
 un              10,049,037     ?    
 mitochondrion   19,517         17
 total           137,586,636    ?     # actually the chromosome lengths sum to 130,450,100

Reads (Drosophila)

 lib                      readLen  #mates    mea,std   ~gc%  %merged(Tanja)   %cChloroplast  %c_Ecoli
 FC70M6V_6_001            160,156  23546475  343,30    42.5                   0.1            12

 TIL_242_FC70M6V_2_002    160,156  9917211   242       .      91.4%  
 TIL_242_FC70M6V_3_002    160,156  6276300   242              92.7%  

 TIL_254_FC70M6V_2_004    160,156  9279789   254        .     91.5%
 TIL_254_FC70M6V_3_004    160,156  5924239   254              92.9%

 TIL_270_FC70M6V_2_003    160,156  10188776  270        .     88.1%
 TIL_270_FC70M6V_3_003    160,156  6556676   270              90.3%

 TIL_288_FC70M6V_2_001    160,156  9524524   288        .     80.0%
 TIL_288_FC70M6V_3_001    160,156  6158919   288              83.0%
  • kastevens@ucdavis.edu:
    • The files labeled TIL_XXX_FC70M6V_Y_00Z, are Drosophila libraries with a median target insert size of XXX. They come in pairs and can be merged.
    • Regarding pairing, each insert size was run in two lanes Y at two different concentrations.
    • Lane 3, with the lower concentration, should have higher quality data than lane 2 but with a higher cost per bp.
    • The loss in quality was quantitativly small, so we don't expect the extra expense of lowering the concentration will be justified empirically.
    • The first library, FC70M6V_6_001, is a ~40x library created from a pool of ~1000 fosmids. In general, we do not put the insert size in the filename.
    • However, we did estimate the insert size to be 343bp with a below median standard deviation of 30. So roughly 15% of the inserts are < 313bp and have > 3bp overlap. This seems to fit well with your result.
    • Each lane is multiplexed into sub-lanes indicated by 00Z. So the amount of reads in the file is variable and not nessesarily reflective of the cluster density.
    • The Drosophila libraries were each run in 1/4 lane and the fosmid pool was run in 1/2 lane. The pool has roughy double the sequence content of the
    • Drosophila libraries run in lane 2 at nominal density.