Specifying Custom hg19 Genome

[phoebe460]

Hello Genrich developers,

First off, thank you for creating a great tool. It's been easy to use so far. I was wondering if there is anyway to input a custom chromosome size file for hg19? For instance, I have this file: hg19.chrom.sizes_new.txt that shows the individual chromosome numbers and sizes that match the headers of my input treatment and control .bed files.

The reason I ask this is when I run Genrich using the following command with parameters: Genrich -t ~/ChIP-seq/BAM_Files/R1039781.nsorted.bam -c ~/ChIP-seq/BAM_Files/NC-Pool.nsorted.bam -o R1039781_q0.10.nsorted.narrowPeak -v -r -y -q 0.10 I don't get any significant peaks and all q values are 1 as shown in my sample output below:

If there is anyway I can use a custom genome file instead (?), then please let me know. Thank you.

[jsh58]

As stated in the README:

Genrich computes the genome length as the sum of the lengths of the chromosomes (reference sequences) in the header of the SAM/BAM file. The length is reduced if the user specifies chromosomes (-e) or genomic regions (-E) to be excluded, as described below.

The only alternative is to specify a genome length via -L <int> as described here.

[phoebe460]

Hi @jsh58,

Thank you for clarifying on how to declare a custom genome length as an alternative approach. I will definitely take a look at this a bit further and see if it will accompany my analysis needs.

All the best, Phoebe