Hi, I'm processing Drosophila data, which contains chrX, chr2L, chr2R, chr3L, chr3R, chr4, chrY, etc. The intron clustering step went ok, but in the output perind_numers.counts.gz file, there's only chr4, chrX and chrY, all other 4 chromosomes are not included. Here is the command I used:
...leafcutter/clustering/leafcutter_cluster_regtools.py -j test_juncfiles.txt -m 50 -o QvsWT -l 500000
Hi, I'm processing Drosophila data, which contains chrX, chr2L, chr2R, chr3L, chr3R, chr4, chrY, etc. The intron clustering step went ok, but in the output perind_numers.counts.gz file, there's only chr4, chrX and chrY, all other 4 chromosomes are not included. Here is the command I used:
...leafcutter/clustering/leafcutter_cluster_regtools.py -j test_juncfiles.txt -m 50 -o QvsWT -l 500000