Question: Analyzing MARS-seq (single-cell RNA seq) fastq files
gravatar for Eldad Shulman
19 months ago by
Eldad Shulman0 wrote:

I am working with fastq files from a single-cell RNA (seq MARS Seq) published on the GEO website GEO: GSE98969. My first goal is to get an expression matrix for each sample , i.e. a matrix U with n rows and m columns, where rows represent genes and columns represent cells. Entry Uij contains the number of UMIs from gene i that were found in cell j.

The problem is that each fastq file contains over 300 cells. The reads are barcoed for cell and for molecule (RMT) in line 1.

I use tophat2 for alignment. I thought about doing th following:
After alignment, per bam file, I'll divide the mapped reads to cells according to cell-barcodes, and will take into account only one count per RMT.

Is there any publicly available tool that you use for this task (which is aware of cell-barcodes and UMIs in the process of generating expression matrix)?

ADD COMMENTlink modified 9 days ago by kkarri0 • written 19 months ago by Eldad Shulman0

Hi Eldad, Just a follow up Were you able to find any solution (tool or code) for processing the MARS-seq single cell data? Because I am in the same situation.

ADD REPLYlink modified 9 days ago • written 9 days ago by kkarri0

Fyi, OP did not log in for 6 months...

ADD REPLYlink written 9 days ago by ATpoint14k
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