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simras / CLAP

CLAP - A pipeline used to process CLIP-seq (specifically PAR-CLIP, HITS-CLIP and iCLIP) data.
MIT License
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Is it possible to use for bacteria? #1

Open tmargus opened 7 years ago

tmargus commented 7 years ago

Hi, I see that CLAP is designed to run on eukaryote genomes. How to adapt it to run on bacteria?

I changed make_annotation.sh by adding species _escherichia_coli_k12 and adjusted ftp site and PATH accordingly. It retrieves annotation and sequence and performs all operations without error message. There are some cosmetic things like Chromosome is converted to "chrChromosome" and some scripts assume 3 command line arguments one of which is "MT" but it doesn't seem to hurt. Is there anything else I should take into account or have to change/modify? Cheers, Tonu

simras commented 7 years ago

Is it not more common for genes to overlap in bacteria?

This could present a problem in the processing of the annotation. Otherwise I cannot think of any reasons it should not work if the organism is well annotated and you check the genome and plasmid names match the sequence files you will use. In the annotation pipeline we rename chromosomes so they match ENSEMBL standard (UCSC chrMT > ENSEMBL chrM).

You can turn off mapping to splice junctions.