I am trying to use leafcutter for differential alternative analysis. As per its requirement, I have generated bam files using STAR.
Now with leafcutter, I have generated bam.juncs and test_juncfiles.txt files successfully using script:
for bamfile in `ls run/geuvadis/*.bam` do echo Converting $bamfile to $bamfile.junc sh ../scripts/bam2junc.sh $bamfile $bamfile.junc echo $bamfile.junc >> test_juncfiles.txt done
Now the next step is intron clustering and differential analysis.
But while doing intron clustering with the script
leafcutter_cluster.py, I am not getting numers.counts.gz files with the format as given in the documentation.
According to documentation file should be in the following format:
RNA.NA06986_CEU.chr1.bam RNA.NA06994_CEU.chr1.bam RNA.NA18486_YRI.chr1.bam RNA.NA06985_CEU.chr1.bam RNA.NA18487_YRI.chr1.bam RNA.NA06989_CEU.chr1.bam RNA.NA06984_CEU.chr1.bam RNA.NA18488_YRI.chr1.bam RNA.NA18489_YRI.chr1.bam RNA.NA18498_YRI.chr1.bam chr1:17055:17233:clu_1 21 13 18 20 17 12 11 8 15 25 chr1:17055:17606:clu_1 4 11 12 7 2 0 5 2 4 4 chr1:17368:17606:clu_1 127 132 128 55 93 90 68 43 112 137
But, Generated counts.gz files contains only my samples name, no other information is present.