how to use custom genome i.e. E. Coli in epic2 ?

Question

[Ankana]

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 <module>
    _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?

[Carlo Yague]

Are the chrosome names exactly the same between the custom genome file and the bam files ?

samtools idxstats SO_4933_A_CHR1_R1_sorted | cut -f 1    # Gives chrom names in bam files
grep -e ">" E.coli_BW25113.fasta                         # Gives chrom names in fasta file