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GWW / scsnv

scSNV Mapping tool for 10X Single Cell Data
MIT License
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Collapsing seg fault? #4

Closed cnk113 closed 3 years ago

cnk113 commented 3 years ago

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:

[00:00:00] Loading the genome
[00:00:07] Loading the transcriptome index
[00:00:07] Loaded 13792 known barcodes from scsnv_barcodes.txt.gz
Segmentation fault (core dumped)

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

GWW commented 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.