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Old 08-26-2014, 03:12 AM   #1
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Question How to create count table for SOAP output?

I would like to use SOAP to align RNA-Seq reads with Rice genome, i have 2 questions :

1- How can i use GTF gene annotation file in SOAP ? (and which version?)
2-How can i create Count table for SOAP output (any software) ?

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Old 08-26-2014, 08:51 AM   #2
Brian Bushnell
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Soap is not designed for RNA-seq alignment, and it does not use GTF files. You'd be better off using a splice-aware aligner such as BBMap, TopHat, or Star.

For determining gene expression, many people use Cufflinks.
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