Hi All,
I computed the raw read counts for one of my SAM files using htdeq-count program as well as using 'countOverlaps' function in IRanges package in R.
CountOverlaps function gives me the read counts for 23123 gene ids.
Output of htseq gives read counts for 35886 refseq ids. (NM as well as NR ids).
After matching the common genes (from CountOverlaps output), I got 32222 genes total from htseq-counts function. I observed that the gene ids were not unique. (21423 unique gene ids.)
The computations were comparable if not same for some of the genes. However, for significant portion of the genes, the raw read counts did not match between the two outputs.
What result is more accurate? Should I sum up the count for same gene id (for htseq-count)?
Can someone please help? I have been stuck with this issue for days now...
thanks a lot.
I computed the raw read counts for one of my SAM files using htdeq-count program as well as using 'countOverlaps' function in IRanges package in R.
CountOverlaps function gives me the read counts for 23123 gene ids.
Output of htseq gives read counts for 35886 refseq ids. (NM as well as NR ids).
After matching the common genes (from CountOverlaps output), I got 32222 genes total from htseq-counts function. I observed that the gene ids were not unique. (21423 unique gene ids.)
The computations were comparable if not same for some of the genes. However, for significant portion of the genes, the raw read counts did not match between the two outputs.
What result is more accurate? Should I sum up the count for same gene id (for htseq-count)?
Can someone please help? I have been stuck with this issue for days now...
thanks a lot.
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