Are there any options for converting bedGraph files to bigwig?
I have a multi-step pipe that takes a bam file, does several operations in a pipe, and currently outputs a bedGraph file. The only option I know of to get from a bed/bedGraph is to UCSC's bedGraphToBigWig
However, this is not compatible with piping so I currently have to save large bedGraph files just to convert them to bigwig in the next step.
Does anyone know how a command that can take bed/bedGraph files and convert to bigwig that also functions in a pipe?
Note: the awk command is simplified for the example, but the steps done are necessary for my purposes so I can't simply go from bam to bigwig.
bedtools bamtobed -i "myfile.bam" \
| awk ' { PRINT } ' \
| bedtools sort -g mygenome.fa.fai \
| bedtools genomecov -i stdin -bg -g mygenome.fa.fai > "myfile.bedGraph"
bedGraphToBigWig myfile.bedGraph chrom.sizes myfile.bigwig
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written
by
RelativeOptics •
1 answer
bedgraphToBigWig performs seek operations on the input file -- so the file must be stored on disk. Nothing you can do with pipes or fifos will get around the fact that these filetypes don't support .seek and will lead to the same error.
If there's some obscure pipe that implements .seek that i don't know about -- use that.
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Not sure but I think you can use the keyWord 'stdin' instead of a filename.
I found a post saying that STDIN cannot me used with bedGraphToBigWig, and I got errors when attempting to pipe into it.
The awk is useless
I mentioned in my post that the awk command is simplified for the example. I only wanted to show that I am using awk to modify a bed file to illustrate that I cannot simply convert bam to bigwig.