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r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq
GNU General Public License v3.0
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barcode files #103

Closed mej54 closed 4 years ago

mej54 commented 4 years ago

Hi,

I'm wondering where/when the barcode files are created (for example: tac_pbmc_5k_nextgem_singlecell.csv)? I've been looking through the documentation/examples for both snaptools and SnapATAC and I can't seem to figure out how to generate these files.

Thank you!

r3fang commented 4 years ago

Hi Molly,

The single cell barcode file is created by cell ranger. The reason that I was using barcode file is because many SnapATAC users have run cell ranger for alignement and basic quality control. This is however not required. You can totally start with a fastq or bam file that does not have barcode file. Let me know if you need help with that

Sent from my iPhone

On Sep 25, 2019, at 2:32 PM, Molly Johnson notifications@github.com wrote:

Hi,

I'm wondering where/when the barcode files are created (for example: tac_pbmc_5k_nextgem_singlecell.csv)? I've been looking through the documentation/examples for both snaptools and SnapATAC and I can't seem to figure out how to generate these files.

Thank you!

Molly — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

mej54 commented 4 years ago

That makes much more sense now. Thank you very much for your response!

qingnanl commented 4 years ago

Hi Molly, The single cell barcode file is created by cell ranger. The reason that I was using barcode file is because many SnapATAC users have run cell ranger for alignement and basic quality control. This is however not required. You can totally start with a fastq or bam file that does not have barcode file. Let me know if you need help with that … Sent from my iPhone On Sep 25, 2019, at 2:32 PM, Molly Johnson @.***> wrote: Hi, I'm wondering where/when the barcode files are created (for example: tac_pbmc_5k_nextgem_singlecell.csv)? I've been looking through the documentation/examples for both snaptools and SnapATAC and I can't seem to figure out how to generate these files. Thank you! Molly — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

To add on to the question, I was using 10x fastq to generate the .snap file. How can I generate the singlecell.csv in that process? I find the information in the metaData of the .snap file, is that correct?

rpique commented 4 years ago

I would like to start without the barcode file, any filtering suggestion?

Hi Molly, The single cell barcode file is created by cell ranger. The reason that I was using barcode file is because many SnapATAC users have run cell ranger for alignement and basic quality control. This is however not required. You can totally start with a fastq or bam file that does not have barcode file. Let me know if you need help with that

r3fang commented 4 years ago

This is redundant with issue 139. I will close this issue, please go to issue 139