search

wheaton5 / souporcell

Clustering scRNAseq by genotypes
MIT License
163 stars 46 forks source link

Splitting mixed-gender single-cell data #186

Open xliu-ucas opened 1 year ago

xliu-ucas commented 1 year ago

Hello, Thank you for providing such a fantastic tool. I have a question.I now have a mixed single-cell sample consisting of four female mice and four male mice. I attempted to split it into eight samples using your software. Here is my command line: nohup /usr/local/bin/singularity exec --cleanenv /data1/xliu/snRNAseq_TRIP4_lung/cellranger/souporcell_latest.sif souporcell_pipeline.py -i possorted_genome_bam.bam -b barcodes.tsv -f /data1/xliu/snRNAseq_NUP214/souporcell/genome.fa -t 20 -o /data1/xliu/snRNAseq_NUP214/souporcell/ -k 8

/data1/xliu/snRNAseq_NUP214/souporcell/souporcell.log 2>&1 However, after splitting, I found that these eight samples do not exhibit differential expression of sex-related genes. This indicates that the splitting was not successful. I'm not sure where the problem lies. I would appreciate your response. Thank you.

suhuanhou commented 1 year ago

I am also processing mixed data. Can you send an email to communicate?

xliu-ucas commented 1 year ago

I am also processing mixed data. Can you send an email to communicate? Very willing to communicate.liuxu221@mails.ucas.ac.cn