Intron Clustering

[JaydenBeckwith]

Hi,

I'm just having some trouble getting intron clustering to work. I have followed the documentation as per instructions and have the junction files for my samples.

However, when I zcat the counts per individual there is no counts per cluster? I have used the default clustering parameters and also have tried other parameters.

Thanks

[jackhump]

Hi! Can you show us the command you used and the error messages generated while clustering?

[JaydenBeckwith]

Hi Jack,

Here are the commands I used, no errors per se (just nothing is clustered in the output) :

for bamfile in *bam; do regtools junctions extract -s 0 -a 1 -m 50 -M 500000 $bamfile -o $bamfile.junc; done

for bamfile in *bam; echo $bamfile.junc >> test_juncfiles.txt; done

clustering counts

python leafcutter_cluster_regtools.py -j test_juncfiles.txt -m 1 -o clusteranalysis -l 500000

zcat clusteranalysis_perind_numers.counts.gz | more

[jackhump]

and just to check, you do have junctions in each file? that's the only thing I could think of that would cause an empty cluster output.

Also, you're using python 3 right? We updated all the scripts in the last year or so.

[JaydenBeckwith]

Hi Jack,

Definitely have junction files - screenshot of one of my samples

That makes more sense - I think I was using python 2.7. I'll check to see if that's the issue

Thanks for your help :)

[Dongmeng-wang]

Hello, I used the latest code for clustering amd also got 0 cluster without any errors. I used python 3.9. Did you fix this problem in your case? Thanks.