Forum: Bioinformatics
07-13-2012, 01:56 PM
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Replies: 2
Views: 3,767
@liueagle, it appears that since bowtie2 by...
@liueagle, it appears that since bowtie2 by default allows less stringent matching (e.g. gaps), the number of mapped reads is higher, but tophat perhaps checks them and makes sure they meet the...
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Forum: Bioinformatics
07-02-2012, 10:15 AM
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Replies: 7
Views: 3,723
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Forum: Bioinformatics
06-29-2012, 02:32 PM
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Replies: 16
Views: 7,300
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Forum: Bioinformatics
06-29-2012, 01:29 PM
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Replies: 16
Views: 7,300
Unfortunately, cuffdiff does not seem to carry...
Unfortunately, cuffdiff does not seem to carry over the original transcript ids from the merged.gtf file in to the output files. However, you can either use Excel (vlookup) or a perlscript or awk to...
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Forum: Bioinformatics
06-27-2012, 02:59 PM
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Replies: 0
Views: 1,105
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Forum: Bioinformatics
06-27-2012, 02:41 PM
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Replies: 2
Views: 1,555
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Forum: Bioinformatics
06-26-2012, 06:44 AM
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Replies: 2
Views: 1,788
@cedance: Thanks for your response. My post...
@cedance: Thanks for your response. My post perhaps was not clear. After the cufflinks run, we use cuffmerge to generate merged gtf and then run cuffdiff on it on each of our bam files. But, I see...
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Forum: Bioinformatics
06-25-2012, 02:49 PM
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Replies: 2
Views: 1,788
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Forum: Bioinformatics
06-21-2012, 02:37 PM
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Replies: 2
Views: 3,767
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