Forum: Bioinformatics
06-01-2015, 09:48 AM
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Replies: 8
Views: 2,512
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Forum: Bioinformatics
05-26-2015, 11:25 PM
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Replies: 15
Views: 6,404
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Forum: Bioinformatics
05-26-2015, 02:12 AM
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Replies: 5
Views: 2,935
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Forum: Bioinformatics
05-26-2015, 01:52 AM
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Replies: 9
Views: 5,348
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Forum: Bioinformatics
05-18-2015, 03:55 AM
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Replies: 8
Views: 2,512
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Forum: Bioinformatics
05-18-2015, 03:22 AM
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Replies: 15
Views: 6,404
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Forum: Bioinformatics
05-21-2013, 04:48 AM
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Replies: 29
Views: 30,158
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Forum: Bioinformatics
02-15-2013, 10:37 AM
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Replies: 14
Views: 2,917
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Forum: Bioinformatics
02-15-2013, 10:29 AM
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Replies: 2
Views: 1,249
I think BEDtools should be able to do this... ...
I think BEDtools should be able to do this...
For instance, you can merge the SNPs/INDELs(using mergeBed), use multiInteresectBed for getting SNPs/INDELs common to all cases, then use subtractBed...
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Forum: Bioinformatics
12-18-2012, 11:18 PM
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Replies: 1
Views: 1,938
Error while running ContEst
I am trying to run ContEst(http://www.broadinstitute.org/cancer/cga/contest)
Below is the command and options I used:
java -Xmx1200m -jar ContEst.jar \
-T Contamination \
-I test.bam...
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Forum: Bioinformatics
12-14-2012, 04:18 AM
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Replies: 7
Views: 22,052
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Forum: Bioinformatics
07-29-2012, 10:15 PM
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Replies: 7
Views: 1,844
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Forum: Bioinformatics
07-22-2012, 08:25 AM
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Replies: 1
Views: 2,954
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Forum: Bioinformatics
07-09-2012, 03:22 AM
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Replies: 2
Views: 4,477
refer to this page...
refer to this page http://picard.sourceforge.net/picard-metric-definitions.shtml#HsMetrics
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Forum: Bioinformatics
07-08-2012, 09:29 PM
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Replies: 6
Views: 2,576
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Forum: Bioinformatics
05-02-2012, 04:48 AM
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Replies: 63
Views: 36,724
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Forum: Bioinformatics
01-18-2012, 01:51 AM
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Replies: 10
Views: 11,320
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Forum: Bioinformatics
11-18-2011, 11:47 PM
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Replies: 15
Views: 6,544
can anybody explain me dis...
many...
can anybody explain me dis...
many SRA(accession) ids having same SRP(study) id this is ok... as justified by an answer above...
but many SRP(study) ids having same SRA(accession) id...?
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Forum: Bioinformatics
11-18-2011, 03:55 AM
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Replies: 15
Views: 6,544
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Forum: Bioinformatics
11-18-2011, 03:34 AM
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Replies: 15
Views: 6,544
I guess I can conclude this:
"NCBI-SRA...
I guess I can conclude this:
"NCBI-SRA doesn't have a single ID using which we can get everything related to it i.e. study, run, experiment, sample", the only way to go about it is use the...
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Forum: Bioinformatics
11-18-2011, 01:06 AM
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Replies: 15
Views: 6,544
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Forum: Bioinformatics
11-17-2011, 03:55 AM
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Replies: 15
Views: 6,544
This is a reply I got from a person in SRA.
...
This is a reply I got from a person in SRA.
The SRA number acts as a collector for the information. This means that when a center submits metadata or data they create a submission (SRAXXXXXX), but...
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Forum: Bioinformatics
11-17-2011, 03:36 AM
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Replies: 15
Views: 6,544
Both link to same page.
I understand SRA...
Both link to same page.
I understand SRA run, they have ID as SRR.
For eg: take this case.
http://www.ncbi.nlm.nih.gov/sra?term=SRA028225
http://www.ncbi.nlm.nih.gov/sra?term=SRA028192...
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Forum: Bioinformatics
11-17-2011, 02:40 AM
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Replies: 15
Views: 6,544
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Forum: Bioinformatics
11-16-2011, 09:26 PM
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Replies: 15
Views: 6,544
Thanx for the reply.
I have checked it but...
Thanx for the reply.
I have checked it but it doesnt contain the information I want i.e. study abstract and description. It only contains IDs, which I already have.
I am trying few other...
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