Bos taurus redo: Difference between revisions
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* [http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&size=0&val=SPECIES_CODE+%3D+%22BOS+TAURUS%22 TA search] | * [http://www.ncbi.nlm.nih.gov/Traces/trace.cgi?cmd=retrieve&size=0&val=SPECIES_CODE+%3D+%22BOS+TAURUS%22 TA search] | ||
* ftp download counts | * ftp download counts | ||
* Avg LEN=984 | |||
* Avg CLIP (CLB intersect CLV)=760 | |||
* Avg CLV=997 (3.66M reads) | |||
* CENTER_NAME counts | * CENTER_NAME counts | ||
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'''37829394''' total total # TA query_tracedb SPECIES_CODE = "BOS TAURUS" => 37,788,710 | '''37829394''' total total # TA query_tracedb SPECIES_CODE = "BOS TAURUS" => 37,788,710 | ||
* TRACE_TYPE_CODE counts | * TRACE_TYPE_CODE counts | ||
Revision as of 16:04, 26 December 2008
BCM
NCBI
- Genome Projects
- TA search
- ftp download counts
- Avg LEN=984
- Avg CLIP (CLB intersect CLV)=760
- Avg CLV=997 (3.66M reads)
- CENTER_NAME counts
COUNT CENTER_NAME 35629020 BCM Baylor College of Medicine 737900 NISC NIH Intramural Sequencing Center 652614 BCCAGSC British Columbia Cancer Agency Genome Sciences Centre # TA query_tracedb CENTER_NAME = "BCCAGSC" => 652,510 378871 MARC USDA, ARS, US Meat Animal Research Center 114753 UIUC University of Illinois at Urbana-Champaign # TA query_tracedb CENTER_NAME = "UIUC" => 106,368 107367 BARC USDA, ARS, Beltsville Agricultural Research Center 65171 TIGR The Institute for Genome Research 53556 GSC Genoscope 43033 CENARGEN Embrapa Genetic Resources and Biotechnology 18623 SC The Sanger Center 15301 UOKNOR University of Oklahoma Norman Campus, Advanced Center for Genome Technology 10651 TIGR_JCVIJTC The Institute for Genomic Research, Traces generated at JCVIJTC # TA query_tracedb CENTER_NAME="JCVI" 2485 UIACBCB University of Iowa Center for Bioinformatics and Computation Biology (UIACBCB) 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) 24863599 BCM WGS 89 31 10748529 BCM SHOTGUN 10 10 737900 NISC SHOTGUN 4 3 125597 BCCAGSC CLONEEND 114753 UIUC CLONEEND 65171 TIGR CLONEEND 53556 GSC CLONEEND 26246 CENARGEN WGS 25454 BARC CLONEEND 16892 BCM CLONEEND 1 1 VBBAA mea=167000 std=25000 16787 CENARGEN CLONEEND 15150 UOKNOR SHOTGUN 10651 TIGR_JCVIJTC CLONEEND 151 UOKNOR FINISHING 49 WUGSC CLONEEND 36809945 total 527017 BCCAGSC EST 207204 MARC EST 171667 MARC PCR 81913 BARC EST 81913 BARC EST 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
- TOTAL and 3' VECTOR TRIMMED counts
CENTER_NAME TRACE_TYPE_CODE TOTAL 3'CLV<LEN BCM WGS 24863599 10968979 BCM SHOTGUN 10748529 5052692 NISC SHOTGUN 737900 28972 BCCAGSC CLONEEND 125597 125484 UIUC CLONEEND 114753 90243 TIGR CLONEEND 65171 46389 GSC CLONEEND 53556 53556 CENARGEN WGS 26246 26246 BARC CLONEEND 25454 25454 BCM CLONEEND 16892 6751 CENARGEN CLONEEND 16787 16787 UOKNOR SHOTGUN 15150 2885 TIGR_JCVIJTC CLONEEND 10651 339 UOKNOR FINISHING 151 ? WUGSC CLONEEND 49 ?
BCCAGSC EST 527017 524173 MARC EST 207204 207204 MARC PCR 171667 171667 BARC EST 81913 78597 SC EST 18623 7350 UIACBCB EST 2485 2485
Data
Local Files:
/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 qaulities
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); "