Closed cnk113 closed 3 years ago
Hi Chang,
Apologies but the read collapsing step only supports alignments generated with scSNV. When I originally designed it I used the alignments from Cell Ranger (which are similar to STAR Solo) but there are certain types of alignment artifacts that made collapsing suboptimal.
Hello,
I've been trying to use the collapse step on a STARSolo output, I was wondering if it's required to run scsnv alignment (BWA based) to get the collapsing to work? I've been trying to run it but I would get a seg fault as such:
Run command:
scsnv collapse -i /media/chang/HDD-1/reference_cellranger/scsnv_index/scsnv-GRCh38-mt-2020-A -r /media/chang/HDD-1/reference_cellranger/refdata-cellranger-arc-GRCh38-mt-2020-A-2.0.0/fasta/genome.fa -o collapse -t 16 -w 16 -b scsnv_barcodes.txt.gz sorted_merged.bam
Best, Chang