Does HTseq need a gtf file that is sorted according to chr number and coordinates?
1 answer
No, htseq-count should work properly, as it did in my case. And FYI, this is from STAR manual :
"With --quantMode GeneCounts option STAR will count number reads per gene while mapping.
A read is counted if it overlaps (1nt or more) one and only one gene. Both ends of the paired-
end read are checked for overlaps. The counts coincide with those produced by htseq-count with
default parameters."
So if you want reads count table equivalent to the one produced by htseq-count in union mode but substantially faster, try that option in STAR. It produces exactly the same counts.
• 0 views
•
link
written
by
grant.hovhannisyan
Log in to answer this question.
More posts like this
-
HTseq count issue, not aligning to features
written by boone5jones •
-
Proper HTSeq usage on bacterial genome. Don't quite understand --t
written by SushiRoll •
-
convert genome coordinates from b36 to hg19
written by @anna •
-
coordinate-sorted versus name-sorted bam file
written by bnayer26 •
-
Sort bam file by coordinates using samtools
written by Shahzad •
-
Ensembl GTF for Mouse that includes intron, exons, utrs, etc.
written by achamess
-
Small rna seq- counting multimapped tRNA fragments
written by grrompala •
-
Has anybody used TEToolkit successfully to quantify transposable elements?
written by Anna S
-
Crucial difference between dexseq and HTSeq-count
written by igolkinaanna11 •
-
Converting Eland Sorted.Export To Eland Results
written by Anna •
'not aligned' means the read is... not aligned.
yes but i thought bowtie would not write the not aligned reads into the sam/bam file so I was surprised by that...
If HTSeq is working as it should then likely no. There must be a reason you are asking this question. Is the counting not working as expected?
You may want to give featureCounts a try instead. It is much faster than HTSeq-count.
okay great thanks for the info, it was sort of working but because I made my gtf it was't sorted properly so just wanted to make sure that this is not a problem :)
Please use
ADD COMMENTorADD REPLYto answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.