[help] Can BSseeker2 handle diploid reference genome please?

[lizhe-gis]

Dear Weilong,

Thank you so much for developing this wonderful tool!

Recently we developed a haplotype-resolved diploid human genome, where one copy is paternal and the other copy is maternal. I am wondering whether BSseeker2 can handle such reference genome please? I imagine if I map WGBS data, most reads will have secondary alignment due to the high similarity of pat-/mat-genome. I understand bowtie2 is able to randomly assign.

Would it be possible to ask BSseeker to randomly assign to one location if the two alignments have exactly the same and highest possible match please?

Thank you very much!

Best Regards,
Zhe

[guoweilong]

Hi Zhe, For the original design of BS-Seeker2, it will only output unique best hit for one read. And the parameter "-M" will be able to output reads with multiple best hits, but only output the information of original reads (maybe you can try to remap them to each of the haplotype). Best, Weilong At 2024-09-06 17:28:15, "lizhe-gis" ***@***.***> wrote: Dear Weilong, Thank you so much for developing this wonderful tool! Recently we have a haplotype-resolved diploid human genome, where one copy is paternal and the other copy is maternal. I am wondering whether BSseeker2 can handle such reference genome please? I imagine if I map WGBS data, most reads will have secondary alignment due to the high similarity of pat-/mat-genome. I understand bowtie2 is able to randomly assign. Would it be possible to ask BSseeker to randomly assign to one location if the two alignments have exactly the same quality score please? Thank you very much! Best Regards, Zhe — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>