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griffithlab / regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.
https://regtools.readthedocs.org
MIT License
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Junction annotation questions #149

Open yanwang271 opened 3 years ago

yanwang271 commented 3 years ago

Hi,

I was using regtools junction annotation to annotate a junction bed file of junction extract output. I found most of the known junctions in GTF file were labeled as "unknown". The junction file was extracted from STAR aligned BAM file and the GTF file was ensemble38.98.

The code I was using is regtools junction extract -a 6 -s 2 sample.bam | regtools junctions annotate -o sample.junc.bed - ref.fa ref.gtf

Could you help me with this?

Regards, Yan

kcotto commented 3 years ago

It sounds like this may be an issue with the strand option you chose. Have you tried running it with -s 1 and seeing if that resolves your issue. Alternatively, if your BAM file has XS tags in it denoting strandedness, you probably want to use the -s 0 option.

capricy commented 2 years ago

Hi Support Team,

I have similar issue. Do you mean: if I use unstranded mode (-s 0) during the extract step, I will have all the junctions as novel?

Thanks a lot.

C.