Question: HTseq or featureCounts without gff file
gravatar for arta
3.6 years ago by
arta620 wrote:


I am doing RNA-seq analysis for allele-specific gene expression. To do that, two mouse strains were hybrid. I do have reference fasta files for both but do no not have gff file for one strain.

So far, I have done the mapping and alignment using STAR and I got Aligned.sortedByCoord.out.bam. Now I would like to compare read counts that are mapped same exons or genes to find allele-specific gene expression. But I am not sure which tool to use. I know both HTseq and featureCounts require gff file. Any ideas ??

sequencing snp rna-seq next-gen • 2.0k views
ADD COMMENTlink modified 3.6 years ago by Devon Ryan98k • written 3.6 years ago by arta620
gravatar for Devon Ryan
3.6 years ago by
Devon Ryan98k
Freiburg, Germany
Devon Ryan98k wrote:

You should be using one of the many available ASE programs rather than trying to roll your own solution.

Anyway, this is what lapels and suspenders are for. You then only need an annotation for one parental line.

ADD COMMENTlink written 3.6 years ago by Devon Ryan98k

Thanks Devon, I will look them.

ADD REPLYlink written 3.6 years ago by arta620
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