When i do the above, i tried to upload it to UCSC genome browser as custom track but it says it cant read my bigwig file.
I converted my bigwig to wig, this time it gives memory error.
Any ideas why this might be happening? or how to fix it?
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Originally posted by id0 View PostThere are several options. I use bedtools genomeCoverageBed to convert from BAM to BedGraph. Then bedGraphToBigWig to convert BedGraph to BigWig.
Maybe someone else knows of a single step option.
1. bedtools genomecov -bg -ibam Mysorted.bam > Mysorted.bedGraph
2. bedgraphToBigWig in.bedGraph chrom.sizes out.bw
At step 2, I am not sure if I understand what is the chrom.sizes file is. Shall i just create one myself simply subtracting end position from the start position to create the chrom.sizes?
I guess 'in.bedGraph' is my Mysorted.bedGraph.
Am i missing something?
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if this is RNA-seq data, be sure to use the -splice option for genomeCoverageBed
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I wrote a Bam2wig : https://github.com/lindenb/jvarkit/wiki/Bam2Wig
It use the cigar elements to get the depth.
( however, I did not often used it)
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There are several options. I use bedtools genomeCoverageBed to convert from BAM to BedGraph. Then bedGraphToBigWig to convert BedGraph to BigWig.
Maybe someone else knows of a single step option.
Leave a comment:
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