XenoCell fq.gz output files

Question

[TC_Chang]

Hi,

I followed the tutorial of XenoCell (see below) and extracted the graft barcodes by using hgmm_5k_v3 example dataset. I got 3 output files (cellular_barcodes.txt, fq_barcode.fq.gz, and fq_transcript.fq.gz) under graft folder. Does anyone know how to convert these files and feed them into 10x genomic cellranger count workflow? Any suggestion will be greatly appreciated.

https://gitlab.com/XenoCell/XenoCell/-/tree/master/examples/hgmm_5k_v3

Best, TC

Answer 1

[Ram]

I know this is late but I was unaware the XenoCell related questions are being posted on the forum here.

Once you're done with the classify and extract_cellular_barcodes steps, create a softlink to the fq_barcode.fq.gz file with a name in the format <sample_identifier>_S1_L001_R1_001.fastq.gz and another soft link to the fq_transcript.fq.gz with a name in the format <sample_identifier>_S1_L001_R2_001.fastq.gz. The absolute path to the directory containing these two links can then be provided as input to CellRanger's --fastqs parameter.

In your case, these commands should work:

cd /path/to/graft/
ln -s fq_barcode.fq.gz mysample_S1_L001_R1_001.fastq.gz
ln -s fq_transcript.fq.gz mysample_S1_L001_R2_001.fastq.gz
cellranger count --id mysample_cellranger --fastqs /path/to/graft/ --transcriptome /path/to/refdata-gex-GRCh38-2020-A/ --sample mysample