could I modify the hg19.chrom.size
Hi,
Can I only keep chr1-21, chrX, chrY, and chrM lines and remove other lines in the hg19.chrom.sizes file? I used STAR to build the index.
When I run bedGraphToBigWig , it reports the error of "GL000191.1 is not found in chromosome sizes file ". Thanks.
Best regards, Yang Chen
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What exactly do you want to do? Filter a bedGraph for those chromosomes?
My workflow is as follows: STAR index -> STAR mapping -> convert bam to bedgraph -> convert bedgraph to bigwig.
When convert bedgraph to bigwig, I think the error may be caused by the hg19.chrom.sizes file.
Yes, obviously this step is the error. Every chromosome in the bg must be in the chromSize file. Therefore, what is the goal? Did you subset the chromSize file?
I hope to get the bigwig file.I am not sure the difference if I only use subset of the chromsize file.
I do not understand what you mean. You can filter out certain chromosomes as you like from the bedGraph using something like
awkbut the chromSize file has to contain all chromosomes included in the bedGraph when converting to bw.If your original reference had only those entries then you could. It is a text file.