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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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create snap file for human and mouse samples #68

Closed znavidi closed 5 years ago

znavidi commented 5 years ago

Hi there,

Thank you for your interesting tool. I have a question regarding whether it is possible to create a snap file for fastq or bam files (or a tsp file) that are samples from both human and mouse data?

Best, Zeinab

r3fang commented 5 years ago

Yes, but can you specify your question

-- Rongxin Fang, Ren Lab Ludwig Cancer Research Bioinformatics Ph.D. Student University of California, San Diego

On Aug 20, 2019, at 2:32 PM, znavidi notifications@github.com wrote:

Hi there,

Thank you for your interesting tool. I have a question regarding whether it is possible to create a snap file for fastq or bam files (or a tsp file) that are samples from both human and mouse data?

Best, Zeinab

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/68?email_source=notifications&email_token=ABT6GG5DRCLFLULT5CYWY5LQFRPHNA5CNFSM4IN5GH42YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HGLNQ7Q, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG3BFP5Z63YSRH6ZMXDQFRPHNANCNFSM4IN5GH4Q.

znavidi commented 5 years ago

Thanks for your prompt answer. Actually I would like to create snap file for https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129785 dataset which has 4 mouse sample files out of all 67 sampels (with probably lots of single cells) and there is a fragments.tsv file in the GEO website that I can create bam file from. I got hg38 as reference file input to snaptools in my first try, but this way I am ignoring mouse data, right? do you have any better suggestion for analyzing this data ?

Best Zeinab

r3fang commented 5 years ago

Hi there,

1) you can actually create the snap file directly from fragments.tsv file, once you sort the fragments based on the barcode column. 2) the genome tag in snap tools is so far useless, it will not filter any fragments.

Best,

Rongxin Fang, Ren Lab Ludwig Cancer Research Bioinformatics Ph.D. Student University of California, San Diego

On Aug 20, 2019, at 2:37 PM, znavidi notifications@github.com wrote:

Thanks for your prompt answer. Actually I would like to create snap file for https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129785 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE129785 dataset which has 4 mouse sample files out of all 67 sampels (with probably lots of single cells) and there is a fragments.tsv file in the GEO website that I can create bam file from. I got hg38 as reference file input to snaptools in my first try, but this way I am ignoring mouse data, right? do you have any better suggestion for analyzing this data ?

Best Zeinab

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/68?email_source=notifications&email_token=ABT6GG27C2S226ZRWBZ3UVDQFRP2FA5CNFSM4IN5GH42YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD4XXU6A#issuecomment-523205240, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GGZ7W6MHBV4VSAN463TQFRP2FANCNFSM4IN5GH4Q.

znavidi commented 5 years ago

Thank You Rongxin :)

Best