I got a bam file and upload to the Galaxy. When I convert it into bigwig, it gives me that message:1 is not found in chromosome sizes file.
Is there somebody can help me with that?
Thank you in advance.
Sounds like a mismatch between between chromosome names, where your bam has e.g. "1", but the dbkey/genome build uses "chr1".
I have a question regarding the IGV and bigwig conversion that maybe you can help me. I am trying to convert a .bam file to bigwig with mouse genome (mm10) to visualize the reads and I am getting this error:
hashMustFindVal: 'GL456210.1' not found
and this is my command:
wigToBigWig -clip mm10.chrom.sizes ./control1.bw
I already found out that I need to convert the chromosome Ids to UCSC. I want to know is this common to convert the IDs from ENSEMBLE to UCSC for bigwig conversion? Do you have any idea about it?
Many Thanks in advance,