Junc files include one strand

[NufarGrinshpan]

Hi,

I am using single end library for my differential splicing analysis. As I use regtools (version 0.5.2, -s 2) to generate junc files it recognize junctions on one strand and not the other. There is no error message but half of the junctions in the file are marked with "?" instead of +/-. how can I fix it?

thanks!

[goldenflaw]

Do you have XS tags in your alignment bam files? I suspect your alignment might not contain this information.

Yang

On Wed, May 3, 2023, 08:07 NufarGrinshpan @.***> wrote:

Hi,

I am using single end library for my differential splicing analysis. As I use regtools (version 0.5.2, -s 2) to generate junc files it recognize junctions on one strand and not the other. There is no error message but half of the junctions in the file are marked with "?" instead of +/-. how can I fix it?

thanks!

— Reply to this email directly, view it on GitHub https://github.com/davidaknowles/leafcutter/issues/234, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABGWTCNJCYR64ADF4EOSYCTXEJJ7VANCNFSM6AAAAAAXUMKWUI . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[NufarGrinshpan]

There is no XS tags (attached an example) but regtools does recognize the strand in approximately half of the introns. The problem is in the bam file?