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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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how to add custome genome #185

Open wangmhan opened 4 years ago

wangmhan commented 4 years ago

Hi,

I work with chicken data. So that I create reference through snaptools index-genome, while fetchChromSizes didn't work so I use .fai file to generate chromesome size.

But encountered problem when I try to snaptools snap-pre, as cannot specify the chicken genome I created. Is there any solution for non model organism?

Thanks a lot! Menghan

plantformatics commented 4 years ago

You can add one ad hoc to file path/to/site-packages/snaptools/global_var.py

tzhu-bio commented 4 years ago

Did you add a custom genome successfully?

wangmhan commented 4 years ago

There is something wrong with the server I used, so didn't got the chance to try yet. I will let you know as soon as I have a try. And the description seems very simple: add one ad hoc to file path/to/site-packages/snaptools/global_var.py. It means that after create index, add the index path to the file: global_var.py. Then it is done. Do I understand correct? Thanks!

On Sun, 17 May 2020 at 10:11, Tao Zhu notifications@github.com wrote:

Did you add a custom genome successfully?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/185#issuecomment-629760063, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJVYTVTRSDOCIL3EUISQOY3RR6L4HANCNFSM4M3MTKJQ .

tzhu-bio commented 4 years ago

Thanks for your reply! You can generate bam files instead of using snaptools. Then using snaptools snap-pre to generate snap file. In this process, the genome parameter is currently not used in the downstream analysis. see details :https://github.com/r3fang/SnapATAC/issues/38

wangmhan commented 4 years ago

Thanks for your reply! I actually used generate bam and snaptools snap-pre, with galGal5. I just didn't get the idea when first time I saw #38. I once thought need to create a genome used the genome name can be recognized first. But now I understand it is actually no matter, as the parameter is not used. Thanks for the instruction!

On Sun, 17 May 2020 at 10:51, Tao Zhu notifications@github.com wrote:

Thanks for your reply! You can generate bam files instead of using snaptools. Then using snaptools snap-pre to generate snap file. In this process, the genome parameter is currently not used in the downstream analysis. see details :#38 https://github.com/r3fang/SnapATAC/issues/38

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/185#issuecomment-629764214, or unsubscribe https://github.com/notifications/unsubscribe-auth/AJVYTVV2JF3OYKYLDPJ4IC3RR6QSDANCNFSM4M3MTKJQ .