Increased number of total exons in DEXSeq
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aditi ▴ 20
@aditi-9925
Last seen 3.1 years ago
Indian Institute of Science,Bangalore, …

Hi,

I have aligned RNA-Seq data from human samples to GRCh37. The flattened file has also been created using the same database using the dexseq_prepare_annotation.py and the counts have been generated using the dexseq_counts.py script. However, the total number of exon for most of the genes are greater than what has been reported in literature. e.g. SNCA, which is reported to have 5 exons shows 26 exons in the analysis and in the flattened file. I have previously worked with the mouse genome using GRCh38 but have not had any issue. What could be going wrong?

Thanks in advance for your suggestions,

Aditi

 

 

dexseq exons grch37 • 713 views
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Hey,

Have a look at the vignette for DEXSeq. The prepare_annotation script flattens all isoforms from the same gene into a single representation of this gene. During this process it creates exonic bins out of the overlapping exons. For example if you have gene with two isoforms and in isoform A the exon goes from coordinate 15 to 50 and in isoform B the exon goes from from coordinate 15 to 25 it will create two bins: exonic_001:15-25 and exonic_002:26:50.

Most likely that's why you have 26 exonic bins.

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aditi ▴ 20
@aditi-9925
Last seen 3.1 years ago
Indian Institute of Science,Bangalore, …

Thanks! How can I solve this?

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Hi, I have the same problem but no idea on how so solve it. I just thought to take out from the .gtf all isoforms but the one of interest...but this way I'll lose lot of info and the "bin problem" will remain in all other genes anyway.

@aditi did you manage to solve the issue then?

Thanks in advance for any suggestion.

Daniele

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