Hi!
I'm using your devel version, so far going very well, thanks!! I'm a bit unsure re optimal choice of references - I noticed in your biorXiv paper you wrote you used 'GRCh38 (GCA_000001405.15), which excludes alternate contigs and decoy sequences from hs38d1' - would that be the version with 195 chromosomes and contigs or the one containing 3366? If I use the one without the decoy sequences, should I modify the file in resources/binned_counts/hg38/bins_mapq60_width1000.bed.gz? if not I get an error Error: requested chromosome chr1_KI270762v1_alt does not exist in the genome file depth_profile/binned_counts/genome_file_for_bedtools.txt. Exiting.
Which one would you recommend?
Many thanks,
Anat
Hi!
I'm using your devel version, so far going very well, thanks!! I'm a bit unsure re optimal choice of references - I noticed in your biorXiv paper you wrote you used 'GRCh38 (GCA_000001405.15), which excludes alternate contigs and decoy sequences from hs38d1' - would that be the version with 195 chromosomes and contigs or the one containing 3366? If I use the one without the decoy sequences, should I modify the file in resources/binned_counts/hg38/bins_mapq60_width1000.bed.gz? if not I get an error
Error: requested chromosome chr1_KI270762v1_alt does not exist in the genome file depth_profile/binned_counts/genome_file_for_bedtools.txt. Exiting.Which one would you recommend?
Many thanks,
Anat