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bedGrapthToBigWig conversion, xxx is not found in chromosome files

Hi, just try to view the result in USCS browser, and when I tried to convert the bedGraph file to bigwig,

it said xxx is not found in chromosome size file.

I wonder whether it is caused by the naming of the entries by different database,

Is there any tool to convert the ID to USCS IDs?

Thanks

chip-seq
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updated by max • max • written by bxia bxia
  • 1) what are the names of the cromosomes in the "chromosome size file. "
  • 2 ) what are the names in your bedGraph
  • 3) compare 1 & 2
  • 4) eureka
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written by Pierre Lindenbaum Pierre Lindenbaum

3 answers

It means that the reference FASTA file you used for alignment and generating bedGraphs is different that the chromosome sizes file.

To generate the chromosome sizes file based on your FASTA file:

samtools faidx genome.fa
cut -f 1,2 genome.fa.fai > chrom.sizes
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written by igor igor

If I use this chrom.sizes,

Will USCS genome browser work?

Thanks

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written by bxia bxia

Yes but only IF you used UCSC's genome sequence to build indexes/align your data.

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written by GenoMax GenoMax

If I am using the indexes from NCBI to map, what should I do now..

and when I try to use bedGraphToBigWig from USCS to convert bedGraph to bigwig, it complained about

End coordinate xxx bigger than xxx...

What should I do..

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written by bxia bxia

If you only want to view your aligned data you can use IGV.

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written by GenoMax GenoMax

another question,

Why I have "End coordinate xxx bigger than xxx..."

I am using the same genome.fa to build chrom.sizes file and build the indexes and map the reads.

I wonder why I have peaks that outside of the edge of the reference genome.

Thanks

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written by bxia bxia

That's usually a sign that you used the wrong genome somewhere. I've only seen that happen when I accidently swappen human and mouse data, for example. I would go back and make sure you used the same one on every step

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written by igor igor

But I only have human genome on my laptop, does MACS parameter relate to this?

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written by bxia bxia

You specify a genome for MACS (by species, not exact FASTA file). I am not sure exactly how it uses that info.

Saying you only have human doesn't mean very much. There are multiple commonly-used and valid human genomes.

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written by igor igor

Tutorial: bedGraphToBigWig Tutorial and Report

bedGraphToBigWig Tutorial and Report

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written by Shicheng Guo Shicheng Guo

Due to history, there are small differences in the way that NCBI, EBI and UCSC name the chromosomes. What is "MT" for EBI, can be "chrMT" for NCBI and "chrM" for UCSC. To convert your NCBI to UCSC chrom names, use UCSC's little utility chromToUcsc. Download it with "wget https://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/chromToUcsc", make it executable with "chmod a+x chromToUcsc" and run it without arguments the usage message. Here is an example call: chromToUcsc -g hg19 --get && chromToUcsc -i test.wig -o test.ucsc.wig -a hg19.chromAlias.tsv -g hg19

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written by max • max

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