Sean Wen

Running Souporcell on multiple BAMs

3

Dear Heaton, I have two 10x BAMs: (1) a cancer patient (2) the same cancer patient after bone marrow transplant. Hence sample 2 would consists of the original patient cells...

Souporcell on plate-based RNA-seq

20

Hi! I hope to run Souporcell on 709 cells generated from plate-based RNA-seq, in lieu of the 10x Genomics in which Souporcell is initially meant for. This dataset consist of...

Somatic variants in vcf

1

I'm interested in tracing previously identified somatic mutation for each single cell. am wondering if the souporcell_merged_sorted_vcf.vcf.gz contains only germline variants or it also contains somatic variants? If the vcf...

Stringtie stopped writing to tmp folder

2

Hi, I'm ran stringtie v2.1.4 and it stopped writing to tmp folder after the .gtf.tmp reached a very specific size (209911808-B). I haven't had any issues with other BAM files...