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davidaknowles / leafcutter

Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard
http://davidaknowles.github.io/leafcutter/
Apache License 2.0
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Empty cluster output #248

Open Dongmeng-wang opened 10 months ago

Dongmeng-wang commented 10 months ago

Hi,

I'm using the up-to-date script leafcutter_cluster_regtools.py to cluster junctions, but I get zero clusters in the output. The python version is 3.11 and the junctions were extracted with regtools. samtools index ${sample}.waspfilter.outblacklist.bam regtools junctions extract -a 8 -m 25 -M 1000000 -s XS ${sample}.waspfilter.outblacklist.bam -o ${outdir}/${sample}.waspfilter.outblacklist.bam.junc

I got 0 clusters from two test files, the script and these two files look like this: image

image

I have gone through a few threads saying that the strand of ? might be the issue. However, our data is unstranded. Can I delete if strand == "?": continue from the script? Actually, I didn't quite get why the junctions with ambiguous strands should be ignored. I would really appreciate it if you could give me a clue about this issue. Thanks!

All the best, Meng

YUTINXIN commented 7 months ago

I have encountered the same problem as you before, because you used the wrong parameter. You can try replacing - s XS with - s RF or - s FR.