creating snap file from fragments.tsv for10X mixture of mouse and human

[znavidi]

Hi,

I am trying to create the snap file like this example: https://github.com/r3fang/SnapATAC/blob/master/examples/10X_P50/README.md but for samples that are mixture of mouse and human data like: https://support.10xgenomics.com/single-cell-atac/datasets/1.0.1/atac_v1_hgmm_500

my question is what should I put for --genome-name and --genome-size arguments.

I really appreciate your help.

Best, Zeinab

[r3fang]

yes.

You can put anything for --genome-name. You need put corresponding genome size file for concatenate genome for --genome-name. For instance,

mm9_chr1 2323 hg19_chr1 2323

It will depend on your concatenate genome.

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

On Aug 23, 2019, at 2:31 PM, znavidi notifications@github.com wrote:

Hi,

I am trying to create the snap file like this example: https://github.com/r3fang/SnapATAC/blob/master/examples/10X_P50/README.md https://github.com/r3fang/SnapATAC/blob/master/examples/10X_P50/README.md but for samples that are mixture of mouse and human data like: https://support.10xgenomics.com/single-cell-atac/datasets/1.0.1/atac_v1_hgmm_500 https://support.10xgenomics.com/single-cell-atac/datasets/1.0.1/atac_v1_hgmm_500 my question is what should I put for --genome-name and --genome-size arguments.

I really appreciate your help.

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/73?email_source=notifications&email_token=ABT6GG4OV37EZT5CKXMBB6DQGBJM7A5CNFSM4IPDPSF2YY3PNVWWK3TUL52HS4DFUVEXG43VMWVGG33NNVSW45C7NFSM4HHEHXYA, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GG6TNX7ZCT3RJP6XD2DQGBJM7ANCNFSM4IPDPSFQ.

[znavidi]

basically, you are saying that I should concatenate the hg38.chrom.sizes and mm10.chrom.sizes files together, right?

[r3fang]

You also need to change the name of the chromosome to make it consistent with your customized concatenate genome

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

On Aug 23, 2019, at 2:36 PM, znavidi notifications@github.com wrote:

basically, you are saying that I should concatenate the hg38.chrom.sizes and mm10.chrom.sizes files together, right?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/r3fang/SnapATAC/issues/73?email_source=notifications&email_token=ABT6GG2X63O7TLW6Z2QY4U3QGBJ4BA5CNFSM4IPDPSF2YY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOD5BMOCQ#issuecomment-524470026, or mute the thread https://github.com/notifications/unsubscribe-auth/ABT6GGZODHD33PLIVPK2RGLQGBJ4BANCNFSM4IPDPSFQ.

[znavidi]

I see! thank you :)