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Jylau14 / hyb2

A program for analyzing proximity ligation experiments from mapped files in the Fastq or SAM format to 1) generate a list of chimeric interactions with their coordinates, sequence, and folding energy, 2) plot contact density map of selected genes, 3) generate intra-/intermolecular RNA structure of any selected regions
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Missing dependency: singularity #7

Closed mwhamgenomics closed 1 year ago

mwhamgenomics commented 1 year ago

The bin/bowtie2 script runs bowtie in singularity, which might not be installed in other systems, and bowtie2 2.3.4.3 is available on Conda anyway. The singularity run command should be replaced with a simple call to bowtie2, and bowtie2=2.3.4.3 should be added to bin/hyb2.yml.

Jylau14 commented 1 year ago

Thank you. I will look at these issues and try to fix them.

mwhamgenomics commented 1 year ago

No problem! From looking at the script again, it refers to locations in the filesystem that don't exist on my system, so it seems to be tailored to a specific system.

It also just runs bowtie2 $@ in the end, so I think this script can be removed. This will make the bowtie2_fast*2sam scripts run bowtie2 directly

Jylau14 commented 1 year ago

Yes, I had a look at the file and deleted it. Thank you!