Convert 10x single cell RNA-seq bam file to bulk RNA-seq bam file
1
1
Entering edit mode
6 months ago
krc3004 ▴ 20

Hi,

Given a sorted bam file from standard 10x cell ranger output, i.e. from https://support.10xgenomics.com/single-cell-vdj/datasets/4.0.0/sc5p_v1p1_hs_PBMC_1k, I am wondering if it's possible to convert this scRNA-seq bam file to a bulk RNA-seq ("pseudo-bulk") bam file, e.g. combining reads across all cell barcodes in the bam file?

I imagine there is a way to do this using samtools, but could not find any examples. Any help would be much appreciated. Thanks!

single cell samtools cell ranger RNA-Seq • 391 views
ADD COMMENT
2
Entering edit mode
6 months ago

It's a normal bam file, just with a few extra tags with cell barcodes and such. You can read more about the tags on the 10X website here. Because there is nothing special about it, you can use any feature counting software designed for RNA-seq, such as Subread or HTSeq.

ADD COMMENT

Login before adding your answer.

Traffic: 2383 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6