BED file : error in naming chromosome's column

Question

[anais1396]

Hello everyone !!

I have a problem with the chromosome's column in my BED files and I'll try to explain that. I have bed files from a peak calling (in format narrowPeak) and in the column chr, we have just the number of the chr that is writting and we need 'chr+the number of the chr' writting.

Let's take an example of my file to be more clear:

File 1: wrong writting in the column chr

chr-number   start-position   end-position   
    1            10003           10454

File 2: good writting in the column chr

chr-number   start-position    end-position
  chr1            10003           10454

I need the first column of my file is writting with 'chr+number of the chr' and not just with the number because I'm doing intersectBed (bedtools) with an other file after the peak caling and this other file is writting with 'chr+the number of the chr' in the chr's column so I have an error message :

ERROR: File some.bed has inconsistent naming convention for record:

1 10003 10454 [...]

Please help me to solve this !! How can I add 'chr' before the number in the fist column of my bed file ?? And I need to add this for each line of my bed file because I've just the number of the chr writting

Thank you in advance !!

Anaïs

[Pierre Lindenbaum]

please validate: C: Problem with the installation of Zinba(peak caller) on R

[anais1396]

Sorry, I forgot !! It's now done

[Pierre Lindenbaum]

please, comment or validate: C: ATAC-seq : strategies to have the list of the expressed genes

[h.mon]

search for awk prepend first column. The answer here will take you to a hairs width from the solution.

Answer 1

[Pierre Lindenbaum]

sed 's/^/chr/'

• How to rename chromosome names in GTF file?
• Human dna reference file with no prefix 'chr'
• ...

[anais1396]

Thank you very much !! It solves my problem !! ;-)

[Pierre Lindenbaum]

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