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biocore-ntnu / epic2

Ultraperformant reimplementation of SICER
https://doi.org/10.1093/bioinformatics/btz232
MIT License
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how to use custom genome i.e. E. Coli in epic2 ? #59

Open Ankana001 opened 2 years ago

Ankana001 commented 2 years ago

Hi, I am using epic2 for my E.coli ChIP-seq data, But it runs with hg19 genome as default, so I used custom genome fasta file which is in the same folder as the data. I am using this following command: epic2 -t SO_4933_A_CHR1_R1_sorted.bam -c SO_4933_A_INR1_R1_sorted.bam --genome E.coli_BW25113.fasta --false-discovery-rate-cutoff 0.001 -a -o SO_4933_A_enriched_regions.csv

But it's showing me error Chromosomes removed from analysis: NZ_CP064677.1 (and 0 more.)

Traceback (most recent call last): File "/home/ibab/.local/bin/epic2", line 257, in _main(args) File "/home/ibab/.local/lib/python3.8/site-packages/epic2/main.py", line 35, in _main effective_genome_length, chromsizes = egl_and_chromsizes(args) File "epic2/src/genome_info.pyx", line 325, in epic2.src.genome_info.egl_and_chromsizes File "epic2/src/genome_info.pyx", line 267, in epic2.src.genome_info.get_effective_genome_fraction KeyError: 'e.coli_bw25113_75.txt'

how to run this analysis with epic2 for E.coli genome?

endrebak commented 2 years ago

You need to use the chromsizes argument where the argument is a file that looks like this: https://github.com/biocore-ntnu/epic2/blob/master/epic2/chromsizes/balAcu1.chromsizes