Via Colette:
Another weird bug from my synthetic genome runs - in order for FLAIR-collapse to work, I had to modify the minimap command as follows:
if not args.quiet:
sys.stderr.write('Aligning reads to reference transcripts\n')
if subprocess.call(['minimap2', '-a', '-t', str(args.t), '-N', '4', '--split-prefix', 'minimap2transcriptomeindex', args.annotation_reliant] + args.r,
stdout=open(args.o+'annotated_transcripts.alignment.sam', 'w'),
stderr=open(args.o+'annotated_transcripts.alignment.mm2_stderr', 'w')):
sys.stderr.write('Minimap2 issue, check stderr file\n')
return 1
The changed bit is the --split-prefix thing. The reason I had to implement it is because I have so many annotated transcripts minimap2 has to make its indices differently. I think the ideal fix for this bug would be to check how many chromosomes (how many lines?) are in the annotated_transcripts.fa file and if they’re over a certain threshold, append the --split-prefix stuff to the minimap command. IDK if there’s any downside to just adding it to the command all the time though
Via Colette: Another weird bug from my synthetic genome runs - in order for FLAIR-collapse to work, I had to modify the minimap command as follows:
The changed bit is the --split-prefix thing. The reason I had to implement it is because I have so many annotated transcripts minimap2 has to make its indices differently. I think the ideal fix for this bug would be to check how many chromosomes (how many lines?) are in the annotated_transcripts.fa file and if they’re over a certain threshold, append the --split-prefix stuff to the minimap command. IDK if there’s any downside to just adding it to the command all the time though