bedGraphToBigWig error in README example

[jmschrei]

Howdy

I was working through the example, and when I got to the following code snippet

# get coverage of 5’ positions of the plus strand
bedtools genomecov -5 -bg -strand + \
        -g hg38.chrom.sizes -ibam merged.bam \
        | sort -k1,1 -k2,2n > plus.bedGraph

# get coverage of 5’ positions of the minus strand
bedtools genomecov -5 -bg -strand - \
        -g hg38.chrom.sizes -ibam merged.bam \
        | sort -k1,1 -k2,2n > minus.bedGraph

# Convert bedGraph files to bigWig files
bedGraphToBigWig plus.bedGraph hg38.chrom.sizes plus.bw
bedGraphToBigWig minus.bedGraph hg38.chrom.sizes minus.bw

I encountered the following error when running bedGraphToBigWig using hg38.chrom.sizes from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes:

chrEBV is not found in chromosome sizes file

[akundaje]

Hmm .. whats the input dataset? It looks like it has reads mapping to the EBV genome (which is part of the lymphoblastoid cell lines).

…

On Wed, Sep 23, 2020 at 3:37 PM Jacob Schreiber ***@***.***> wrote: Howdy I was working through the example, and when I got to the following code snippet # get coverage of 5’ positions of the plus strand bedtools genomecov -5 -bg -strand + \ -g hg38.chrom.sizes -ibam merged.bam \ | sort -k1,1 -k2,2n > plus.bedGraph # get coverage of 5’ positions of the minus strand bedtools genomecov -5 -bg -strand - \ -g hg38.chrom.sizes -ibam merged.bam \ | sort -k1,1 -k2,2n > minus.bedGraph # Convert bedGraph files to bigWig files bedGraphToBigWig plus.bedGraph hg38.chrom.sizes plus.bw bedGraphToBigWig minus.bedGraph hg38.chrom.sizes minus.bw I encountered the following error when running bedGraphToBigWig using hg38.chrom.sizes from http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes: chrEBV is not found in chromosome sizes file — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#2>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABDWEO6T5ELKFBLM3ZABT3SHJ2A5ANCNFSM4RXSV5IQ> .

[jmschrei]

This is the experiment used in the README example: https://www.encodeproject.org/experiments/ENCSR000EGM/ It's CTCF in K562.

[zahoorz]

@jmschrei try using this chrom sizes file https://github.com/ENCODE-DCC/encValData/blob/master/GRCh38/GRCh38_EBV.chrom.sizes