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Old 01-15-2016, 05:11 AM   #1
Senior Member
Location: UK

Join Date: Feb 2014
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Default RNA-Seq: GFOLD counts is different from HTSeq-count

Does anybody use GFOLD before?

Why do I use these two tools count reads but give different results?

In GFOLD manual, “Because of possible overlapping of multiple genes, a read could be mapped to the overlaped region of multiple genes. In this case, a read is counted multiple times with each time for each gene. Furthermore, if a gene is on multiple chromosomes or different strands of the same chromosome, only exons on one strand of one chromosome (the one appear first in the annotation file) will be assigned to this gene. Exons not on this strand of the chromosome will be discarded.”

gfold count -ann genes.gtf -tag sample1.sam -o sample1.read_cnt

htseq-count --minaqual=10 --mode union sample1.sam genes.gtf>htseq.counts
Is that because HTSeq skip the alignment quality lower reads?
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Old 01-15-2016, 05:28 AM   #2
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

The part you showed from the GFOLD manual is completely different from what htseq-count and featureCounts do, so it's expected that you'd get different results.
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