DEXseq reads all in ambiguous_readpair_position and empty categories
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514028929 • 0
@514028929-13268
Last seen 5.9 years ago

 

Hi there,

I am having problem with the DEXseq package.

I want to test if the exon usage of honey bee (Apis mellifera) has changed after infection.

As the DEXseq package suggests, I downloaded the honey bee genome fasta file and the annotation gff file from ensembl website, but I cannot find the gtf file from ensembl. 

Thus, it seems I cannot create the annotation file which specific use for the DEXseq package and I tried the gtf file from the NCBI by using dexseq_prepare_annotation.py script.

However, after create the DEXseq annotation gff file, I use dexseq_count.py to count the reads.

ALL the reads are in the ambiguous_readpair_position and empty categories.

I tried different combinations of the annotation file and the genome fasta, still the same thing happened.

Can somebody give me some tips on this ? 

Thank you in advance!!!

 

dexseq reads • 1.2k views
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I would make sure that the chromosome names are in the same format between your alignments files and the gtf file. A read pair is classified as ambiguous when it maps to two different exon features, don't see an obvious explanation for this, but maybe after checking the chromosome names this will improve? 

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