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kundajelab / basepairmodels

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bedGraphToBigWig error in README example #2

Open jmschrei opened 3 years ago

jmschrei commented 3 years ago

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 commented 3 years ago

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 notifications@github.com 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

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jmschrei commented 3 years ago

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

zahoorz commented 3 years ago

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