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mortazavilab / lapa

Alternative polyadenylation detection from diverse data sources such as 3'-seq, long-read and short-reads.
https://www.biorxiv.org/content/10.1101/2022.11.08.515683v1
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output files #9

Closed peterthorpe5 closed 2 years ago

peterthorpe5 commented 2 years ago

Dear Lapa,

I have run your tool, currently as a test. I was wondering if you could add some documentation/ pass on some wisdom on what output files to expect?

I have bw and bed files for all my conditions. I have polyA_cluster.bed (what do the columns stand for? What does "None@None" in the last columns mean? .

I have no other files ... ... I was wondering if the program terminated early, however, there is no error or warning in any out files via slurm .. (RAM limit was not exceeded)

can you please advise?

Kind regards,

Pete

MuhammedHasan commented 2 years ago

Thanks for your interest in LAPA. I am working on the new release of LAPA 0.0.3 will be out next week when I add more documentation.

peterthorpe5 commented 2 years ago

Hi Muhammed,

I was wondering if there was some more documentation on the output file (even column headers please)? I have results and I am keen to understand them. :)

Is this on a dev branch?

regards, Pete

MuhammedHasan commented 2 years ago

Hi Peter,

Thanks for your interest and patience. I released version 0.0.3 of LAPA, which is the stable version of the package. Also, documentation is added for output format: https://lapa.readthedocs.io/en/tss_clustering/output.html

I highly recommend you rerun the new version where I implemented new features to improve cluster calling especially filtering for replication.

Thanks for your interest.