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Hi,
I've been using Hisat2 to align unstranded RNAseq data. Most of the junction reads were with XS tags. I am also aware of XS tags only reported for canonical splice sites. However, I did see a gene of interest (see the attached file) have 710 splice reads in CD4SP and 798 splice reads in CD8SP spanning the last junction (from right to left: 5'->3') with a non-cannocial splice site. Due to the absences of XS tags in these junction reads, Stringtie excluded them when assembling transcripts. As you can see, these are lots of reads and also supported by the upstream and downstream exonic reads. It doesn't seem right to me to just exclude them.
Is there any way to get HISAT2 to put XS tags on non-canonical splice junctions? Thanks!
The text was updated successfully, but these errors were encountered:
Hi,
I've been using Hisat2 to align unstranded RNAseq data. Most of the junction reads were with XS tags. I am also aware of XS tags only reported for canonical splice sites. However, I did see a gene of interest (see the attached file) have 710 splice reads in CD4SP and 798 splice reads in CD8SP spanning the last junction (from right to left: 5'->3') with a non-cannocial splice site. Due to the absences of XS tags in these junction reads, Stringtie excluded them when assembling transcripts. As you can see, these are lots of reads and also supported by the upstream and downstream exonic reads. It doesn't seem right to me to just exclude them.
Is there any way to get HISAT2 to put XS tags on non-canonical splice junctions? Thanks!
The text was updated successfully, but these errors were encountered: