Add resistance gene depth qc #14
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dfornika
requested changes
Sep 27, 2023
bin/calculate_res_gene_depth_qc.py
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| for line in bed_file: | ||
| fields = line.strip().split() | ||
| gene_name = fields[3] | ||
| start_position = int(fields[1]) |
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I think we may need to add 1 to the start position in the bed file to make it consistent with the start position in the depths file.
https://www.htslib.org/doc/samtools-mpileup.html#Pileup_Format
https://en.wikipedia.org/wiki/BED_(file_format)
https://en.wikipedia.org/wiki/General_feature_format
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Sounds good, fixed here
dfornika
requested changes
Sep 27, 2023
dfornika
approved these changes
Sep 27, 2023
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solution for calculating gene coverage from #12
Note: double check calculate_res_gene_depth.py is indexing the genome position correctly and confirm calculation is correct for one sample/gene before merging.