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Forum: RNA Sequencing 12-10-2012, 10:09 AM
Replies: 6
Views: 2,536
Posted By ajgentles
I found that if you tell tophat2 to generate a ...

I found that if you tell tophat2 to generate a
transcriptome index by supplying a GTF file, but the index already
exists, it bombs out. You have to make sure not to tell it the GTF file
again. ...
Forum: RNA Sequencing 07-12-2012, 09:08 AM
Replies: 6
Views: 2,536
Posted By ajgentles
tophat2/samtools

We have been trying to move from tophat1 to tophat2 utilizing a transcriptome as well as genome reference, and are having some performance and output issues. RNA-seq data that previously took about...
Forum: RNA Sequencing 03-01-2012, 08:40 AM
Replies: 37
Views: 19,635
Posted By ajgentles
I don't think so - the reported length including...

I don't think so - the reported length including the adapters is >400 bp. Given that the reads appear to overlap, it's not clear to me what to tell tophat for the mate pair inner distance. Does it...
Forum: RNA Sequencing 02-29-2012, 08:47 PM
Replies: 37
Views: 19,635
Posted By ajgentles
unexpectedly small ineset sizes

Thanks for the description on estimating insert-size with bwa and picard. I just tried it with some data we have and am a bit surprised by the results. Bioanalyzer results on the sample suggested...
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