how to solve this problem in bedtools genomecov?

Question

[Lila M]

Hi everybody, I'm trying to overlap a list of initiation zones from mouse to the mouse genome. The initiation zone looks like this

chr1    10029400    10030599
chr1    10041200    10042599
chr1    10115200    10116199
chr1    10117800    10118799
chr1    102076400   102077399
chr1    10221800    10224199

And the genome was downloaded from USCS http://genome.ucsc.edu/cgi-bin/hgTables

#name   chrom   strand  txStart txEnd   cdsStart    cdsEnd  exonCount   exonStarts  exonEnds    proteinID   alignID
ENSMUST00000193812.1    chr1    +   3073252 3074322 3073252 3073252 1   3073252,    3074322,        uc287gdb.1
ENSMUST00000082908.1    chr1    +   3102015 3102125 3102015 3102015 1   3102015,    3102125,        uc287gdc.1
ENSMUST00000159265.1    chr1    -   3206522 3215632 3206522 3206522 2   3206522,3213438,    3207317,3215632,        uc007aet.2

I'm using this command line to get my output: b

bedtools genomecov -d -split -i initiation_zone_sort.bed -g mm10.gencodevm20.txt > mm10.vM20.genomecoverage

But I get this error: Input error: Chromosome chr1 found in your input file but not in your genome file

Any ideas? Thanks!

[Bastien Hervé]

bedtools genomecov -h
Notes: 
    (1) The genome file should tab delimited and structured as follows:
    <chromName><TAB><chromSize>

    For example, Human (hg19):
    chr1    249250621
    chr2    243199373
    ...
    chr18_gl000207_random   4262

Answer 1

[ATpoint]

This is not a genome file in terms of what bedtools genomecov expects as genome. genome is a tab-delimited file with column1 the chromosome name and column2 its length (=sum of total basepairs of that chromosome).

=> As you want the coverage over a set of regions, look at bedtools coverage. genomecov will produce a coverage profile over the entire genome. What you downloaded is also not an accepted file format for bedtools. It requires either BED or GTF. You will have to transform this file into either of these. Can be done with awk.

[Lila M]

with gtf file I have the same error...

[ATpoint]

As I said you cannot use any of those with genomecov you need coverage.

[Lila M]

Yes, I as I said, running bedtools coverage -a initiation_zone_sort.bed -b gencode.vM20.annotation.gtf > mm10.vM20.genomecoverage I get the error Error: The genome file gencode.vM20.annotation.gtf has no valid entries. Exiting.

[ATpoint]

Is that 100% of the command line you used? The error refers to option -g which you did not specify.

[Lila M]

Yes it was, but after checking the files I found a mistake in the gft one. Now it works perfectly! Thanks for the advice!