snaptools dex-fastq input argument 10x barcodes

r3fang / SnapATAC

Analysis Pipeline for Single Cell ATAC-seq

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snaptools dex-fastq input argument 10x barcodes #15

Closed smanne07 closed 5 years ago

smanne07 commented 5 years ago

Hi, I had a question about the --index-fastq-list argument to dex-fastq command,is this input a file with cell indices like 10x barcode file for 10x fastq files?

I wanted to make sure it is actually R2 file instead of I1 file ,the tutorial here says I1(https://github.com/r3fang/SnapATAC/wiki/FAQs#CEMBA_snap).

Best regards Sasi

r3fang commented 5 years ago

Hi Sasi,

The tutorial you have pointed to is not 10X single cell ATAC-seq. The barcode design is quite different from 10X dataset. Please refer to this example for demultiplexing for 10X dataset

https://github.com/r3fang/SnapATAC/blob/master/examples/10X_P50/README.md

Best, -R

smanne07 commented 5 years ago

Thank you for clarifying!

The tutorial i pointed has 10x subsection(How to create snap file from 10X dataset?),so was confused.

r3fang commented 5 years ago

Sorry. should have made it more clear