Forum: Bioinformatics
08-07-2014, 07:00 PM
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Replies: 0
Views: 1,366
beagle input format
Hello All,
I am trying to impute using beagle 4 and was wondering how the vcf file has to be formatted. I did get the reference or phase file formatted and am having trouble with imputation...
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Forum: Bioinformatics
09-25-2013, 08:54 AM
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Replies: 2
Views: 1,663
True to some extent as i have tried GSNAP vs...
True to some extent as i have tried GSNAP vs Tophat vs CLC. But what baffles me are the differences in numbers. What would happen if you are working on depth of coverage data and how would one...
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Forum: Bioinformatics
09-24-2013, 07:18 PM
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Replies: 26
Views: 16,066
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Forum: Bioinformatics
09-24-2013, 02:05 PM
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Replies: 2
Views: 1,663
CLC vs tophat: differences is alignment?
Hi
I have been using CLC for sometime and was wondering if any one has compared metrics between CLC and other aligners.
I found something interesting and wanted to know if anybody has...
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Forum: Bioinformatics
09-24-2013, 02:03 PM
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Replies: 26
Views: 16,066
Hi
I have been using CLC for sometime and...
Hi
I have been using CLC for sometime and was wondering if any one has compared metrics between CLC and other aligners.
I found something interesting and wanted to know if anybody has...
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Forum: Bioinformatics
09-05-2013, 09:46 AM
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Replies: 28
Views: 5,512
GMAP and HTseq problems
I use GMAP to align my RNA-seq and then I use HT-Seq to get the counts. When i run the HTseq count script, it always complains of the sam file not being sorted.
I have used from picard tools,...
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Forum: Bioinformatics
08-10-2013, 07:59 PM
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Replies: 0
Views: 750
GATK ? How to out put all read numbers
Hi,
I have a question regarding GATK. I am trying to get SNP calls and the number of reads associated with it (AD). When i look at the data, the number reads is no greater than 99 either for...
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Forum: Bioinformatics
06-14-2013, 06:25 AM
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Replies: 6
Views: 2,880
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Forum: Bioinformatics
06-14-2013, 06:19 AM
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Replies: 1
Views: 1,548
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Forum: Bioinformatics
06-12-2013, 10:01 AM
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Replies: 1
Views: 1,548
Freebayes 0.9.9 problems
Hello All,
I am trying to run freebayes version 0.9.9 and am having problems. I am used pervious versions and never encountered these problems.
The command is use:
freebayes -XuiP 0.01 -f...
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Forum: Bioinformatics
06-12-2013, 09:38 AM
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Replies: 6
Views: 2,880
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Forum: Bioinformatics
07-16-2012, 06:47 PM
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Replies: 2
Views: 2,028
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Forum: Bioinformatics
07-11-2012, 09:25 AM
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Replies: 2
Views: 2,028
Who is the culprit? Picard, Samtools or GATK?
hi,
I am using RNA-Seq data and my work flow is below..and am having trouble with BAM file
Single end fastq->Shrimp alignment->sam file->changed to BAM using Samtools->added read groups using...
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Forum: Bioinformatics
07-11-2012, 09:13 AM
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Replies: 6
Views: 4,434
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Forum: Bioinformatics
07-11-2012, 09:00 AM
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Replies: 6
Views: 4,434
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Forum: Bioinformatics
07-09-2012, 05:43 PM
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Replies: 7
Views: 3,161
thanks for the help. Yes, i do have two...
thanks for the help. Yes, i do have two populations that i need to call the SNPs. I am sure your method works, but i will keep it as an last resort. But its a such as shame that such a useful tool is...
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Forum: Bioinformatics
07-09-2012, 05:29 PM
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Replies: 7
Views: 3,161
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Forum: Bioinformatics
07-09-2012, 04:51 PM
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Replies: 7
Views: 3,161
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Forum: Bioinformatics
07-09-2012, 04:35 PM
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Replies: 7
Views: 3,161
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Forum: Bioinformatics
07-01-2012, 02:51 AM
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Replies: 9
Views: 2,794
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Forum: Bioinformatics
06-29-2012, 11:40 AM
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Replies: 9
Views: 2,794
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Forum: Bioinformatics
06-29-2012, 09:41 AM
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Replies: 9
Views: 2,794
samtools view file.bam | grep...
samtools view file.bam | grep "HWI-ST913:105:C0EYJACXX:5:1304:11235:16705" > bad_read.sam
Output. looks like there is * instead of quality score. Now have to check fastq file....
...
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Forum: Bioinformatics
06-29-2012, 09:08 AM
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Replies: 9
Views: 2,794
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Forum: Bioinformatics
06-29-2012, 08:08 AM
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Replies: 9
Views: 2,794
I did find something.
This problem is only...
I did find something.
This problem is only with Tophat based BAM files. I have a SHRIMP based BAM alignment and GATK works like a charm. Can any one shed some information as to why?
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Forum: Bioinformatics
06-29-2012, 06:36 AM
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Replies: 9
Views: 2,794
GATK BAM error
Hi
I am having trouble with GATK ability to read my BAM files. THe BAM were created using tophat 2.0.0.4 and I used AddandReplaceReadGroups from Picard tools to do it. The code used was
java...
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