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Old 07-21-2015, 10:05 AM   #1
Location: Germany

Join Date: Mar 2011
Posts: 68
Default alternative for HTSeq

We sequenced RNA for one organism with a very incomplete reference sequence. So we had to map against nearly 6000 contigs. Nevertheless we would like to investigate differentially expressed genes with DeSeq. Unfortunately, it seems that HTSeq can't handle such a high number of contigs and annotated genes. Are there any other programs, which we could use to calculate the read count per gene?
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Old 07-21-2015, 10:10 AM   #2
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Give featureCounts a try.

Latest version of STAR also implements a quant option like htseq-count.
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