TU Filter error at TU calling step

shaorray / TU_filter

A local TU annotation tool for multi-sample comparison

GNU General Public License v3.0

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Open aswathyseb opened 10 months ago

aswathyseb commented 10 months ago

I am reopening this issue #5 since I still get this error.

I do have STAN (v 2.26.2) installed and I was able to run a stand-alone STAN script.

I have attached the session info here.

The error is Warning: Error in [[<-: 1 elements in value to replace 0 elements

What else do you think might be the problem? I would really like to see the app running.

Thanks,

shaorray commented 10 months ago

HI,

Sorry, I couldn't repeat this error. It seems to be a rare case of missing element, maybe from ncRNA types or chromosomes.

Did you notice at which step the app stops?

Or have you run directly with TU.gff (upload in page2) (example) without a bam file input?

Best,

aswathyseb commented 10 months ago

I am using the mouse GTF file from Ensembl along with my bam files as the input.

It stops immediately after starting the TU calling step.

I made a test data set with just chr1 in the bam file and annotation file and tried running. But I get the same error.

My input files are here

aswathyseb commented 9 months ago

I just wanted to let you know that I figured what the problem was.

TU Filter expects chromosomes to be named as chr1, chr2 etc.

I was using an Ensembl based reference which has chromosome names as 1,2 etc.

Changing to chr1, chr2 naming fixed the issue.

It would be great if the program can take both naming schemes in its input file though.

Thanks,

shaorray commented 9 months ago

Hi,

It's nice that you solve it, and a surprise to find the chromosome style fails adjustment. (at #1056)

I still cannot repeat this issue with GRCm39.111 in 1,2,3... chromosome name, but a safe check of the style will be added.

Thanks!