Question: htseq read counts zero
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17 months ago by
fate.gh10 wrote:


I have imported some fastq files (homo sapiens) from to Galaxy. In order to obtain read counts, I aligned them to hg19 using HiSat (default parameters). Then since my reference genome was hg19, I used GTF file (Version 19 (July 2013 freeze, GRCh37) - Ensembl 74, 75) from Gencode to obtain read counts using htseq.

The total number of counts obtained for features is "10347508" which seems to be ok. While I have lost a number of counts about

__no_feature 2362227 __ambiguous 788874 __too_low_aQual 1001993 __not_aligned 2517255 __alignment_not_unique 3866370

Do you think the result is reasonable?

Something confusing is that from total 57820 genes, the counts for each gene up to gene 18356 are mostly non-zero, but counts for each gene from gene 18356 to gene 57820 are mostly zero (a few of them are non-zero).

Why is that?

Do you think I have to change my GTF file? Which version?

Or do you think I have to consider only the first 18356 genes for DE analysis ?


ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson24k • written 17 months ago by fate.gh10
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17 months ago by
United States
Jennifer Hillman Jackson24k wrote:


Check for a mismatch between the chromosome names in the inputs. This prior Q&A explains:

A reference GTF file for hg19 with chromosome identifiers that match the natively indexed hg19 can be obtained from UCSC or iGenomes.

Best, Jen, Galaxy team

ADD COMMENTlink modified 8 months ago • written 17 months ago by Jennifer Hillman Jackson24k
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