Hi everyone,
it is the first time that I try to visualize my data on the UCSC Genome Browser.
I am not so familiar with the data format required for custom track visualization so I have followed some indications from papers, manuals etc...
I have 20 RNAseq samples (2x75, ~60 mil reads each, Homo Sapiens).
here's the pipeline I have followed:
bedtools bamtobed -split -i accepted_hits.bam > accepted_hits.bed
sort -k 1,1 accepted_hits.bed > sorted.accepted_hits.bed
bedtools genomecov -i sorted.accepted_hits.bed -bg -scale 10 -g chrom.sizes > normalized.bg ###so that I could normalize for 10 RPM###
bedGraphToBigWig normalized.bg chrom.sizes mybigwig.bw
The file are uploaded on the genome browser and I don't see any error message BUT I don't see anything at all...zero!
I am almost sure I have done something very stupid, maybe in creating the files or during the visualization process.
Can anyone help???
Thanks!
Manu
it is the first time that I try to visualize my data on the UCSC Genome Browser.
I am not so familiar with the data format required for custom track visualization so I have followed some indications from papers, manuals etc...
I have 20 RNAseq samples (2x75, ~60 mil reads each, Homo Sapiens).
here's the pipeline I have followed:
bedtools bamtobed -split -i accepted_hits.bam > accepted_hits.bed
sort -k 1,1 accepted_hits.bed > sorted.accepted_hits.bed
bedtools genomecov -i sorted.accepted_hits.bed -bg -scale 10 -g chrom.sizes > normalized.bg ###so that I could normalize for 10 RPM###
bedGraphToBigWig normalized.bg chrom.sizes mybigwig.bw
The file are uploaded on the genome browser and I don't see any error message BUT I don't see anything at all...zero!
I am almost sure I have done something very stupid, maybe in creating the files or during the visualization process.
Can anyone help???
Thanks!
Manu
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