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.
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
Genrichusing 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 0.10I 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.