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EnvGen / toolbox

Various scripts used at the EnvGen group, directed towards metagenomic analysis.
MIT License
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Does input_table.py script for kallisto to concoct assume 200bp reads? #8

Open franciscozorrilla opened 4 years ago

franciscozorrilla commented 4 years ago

Hi, I was looking into the above mentioned script (https://github.com/EnvGen/toolbox/blob/master/scripts/kallisto_concoct/input_table.py), and I was wondering about line 31:

kallisto_df['kallisto_coverage_{0}'.format(sample)] = 200*sample_df['est_counts'].divide(sample_df['length'])

Does this assume 200bp reads, and if not, what is the significance of the 200 factor? Would input tables generated with this script for 100 bp or 150 bp datasets result in unreliable/inaccurate abundance estimates?

Best wishes, FZ

alneberg commented 4 years ago

Hi @franciscozorrilla, yes you're correct, the script assumes 200bp reads. This should not be a problem for other read lengths however, it's mostly used to generate a comparable number which is given from the mapping. Feel free to change the number in a copy of the script to your liking.