brianjohnhaas
commented
2 months ago Hi Arda,
The read name formatting cellbarcode^UMI^read_name is needed to get the single cell reporting. If you're starting from fastqs, hopefully there's info somewhere from the data source that would indicate where the metadata is that provides the UMI and cell barcode info. Once you have that, you could use something like pysam or a simple python script to format the fastqs. I don't have a general script for this other than what's typical of 10x ubams, as provided from the documentation.
On Thu, Jul 11, 2024 at 2:54 PM Diren Arda Karaoglu < @.***> wrote:
Hi CTAT-Mutations Team, Thanks for the awesome package! I've had great success using CTAT-Mutations with my bulk RNAseq data, and now I'm looking to give it a try with my single-cell RNAseq data. I'm running into a bit of a problem with the fastq file format. The tutorial mentions that the read names need to be in this format: cellbarcode^UMI^read_name. There's a script provided for converting from ubam files, but like many others, I get my fastq files straight from the sequencing core. I tried editing the files myself, but I couldn't get the format right. Do you have a script for fastq files? Or can you provide more details on how read1 and read2 should look? Thanks a lot for your help! Best, Arda
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Brian J. Haas The Broad Institute http://broadinstitute.org/~bhaas http://broad.mit.edu/~bhaas
direnardak
Hi CTAT-Mutations Team, Thanks for the awesome package! I've had great success using CTAT-Mutations with my bulk RNAseq data, and now I'm looking to give it a try with my single-cell RNAseq data. I'm running into a bit of a problem with the fastq file format. The tutorial mentions that the read names need to be in this format: cellbarcode^UMI^read_name. There's a script provided for converting from ubam files, but like many others, I get my fastq files straight from the sequencing core. I tried editing the files myself, but I couldn't get the format right. Do you have a script for fastq files? Or can you provide more details on how read1 and read2 should look? Thanks a lot for your help! Best, Arda