Entering edit mode
3.7 years ago
sidrah.maryam
▴
50
Hello everyone, I have single end sequence fastq files that were processed using cellranger. Now I need to align them using cellranger count function. But being single end, the naming convention followed could not be standard. Is there a way to do so? I tried using SRR9320581_S1_L001_R1_001.fastq.gz file convention, but it gave pipestance failed error.
Any help is highly appreciated. Thank you
cellranger count
needs files in a special format. There are three separate files (if you have > 1 sample).R1
file contains the cell barcodes and UMI,I1
file contains Illumina index for the sample,R2
file contains actual reads. It appears that these investigators may have submitted these fastq files in a concatenated format. Try to see if you can separate the reads using--split-files
option forfastq-dump
.okay. I will try that. Thanks a lot.
I have the same issue, did the split-files solved your problem ?
Just my two cents here. In my case
cellranger count
was failing becauseR1
was in the wrong format. I also had single-end reads, whereR1
was supposed to be the cell barcode and UMI, andR2
should be the single-end reads. In my case I had to reruncellranger mkfastq
from the raw BCLs. Note that theI1
file mentioned is optional forcellranger count
so don't worry if you don't have it.In my experience the
--split-files
option forfastq-dump
is only relevant if you're downloading data from SRA, not if you have your raw data in-house.Please read the question - OP has SRR identifiers, hence their data is from SRA. That is why GenoMax mentioned the
--split-files
.