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BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA
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no .bed out from flair.py align #206

Closed MustafaElshani closed 2 years ago

MustafaElshani commented 2 years ago

Using latest builds there are no .bed files in the output folder from running flair.py align, running latest samtools version 1.15.1. In addition, there are no sorted .bam files either.

the only files I get is .psl .sam .unsorted.bam and unsorted.bam.stderr

Any help is very much appreciated

Kind Regards

MustafaElshani commented 2 years ago

This seems to resolve with -v1.3 Maybe this should be arranged to accommodate only latest samtools since v1.3 is now old

Jeltje commented 2 years ago

Thank you for this bug report. I have updated the code to improve version checking, it should now work with all samtools versions >= 1.3. We will soon do a new release that includes this fix. If you want to start using the latest version, please git clone git@github.com:BrooksLabUCSC/flair.git

Please reopen this ticket if this does not solve your problem.