Chromosome naming in bigwig files

[Jeremy Day]

Hello,

I have been using DeepTools for visualization of some NGS data generated in my lab, using the DeepTools Galaxy interface. I am having some trouble with a recurring warning that occurs when I create a matrix using a bed file that contains gene tracks from all chromosomes of the rat Rn5 assembly. I have pasted the warning below, in red text. Unfortunately it does not seem to like that the bed file refers to the X chromosome as chrX. However, this seems to be the nomenclature everywhere else, and so I am not sure what it is looking for. Is it possible that the name for the X chromosome in my BAM file is different than chrX?

  Warning: Your chromosome names do not match. Please check that the chromosome names in your BED file correspond to the names in your bigWig file. An empty line will be added you your heatmap. The offending chromosome name is chrX.

Thanks for your help. 

Jeremy

[Fidel Ramirez]

Hi Jeremy,

It is frequent that the chromosome X is often referred simply as X (and so on for other chromosomes). Thus, a simple fix is to remove in the BED file all 'chr'. You can use the Text Manipulation -> Trim Galaxy tool for this. In the field: Trim from the beginning up to this position, choose 4 to remove the first three characters of each line of the file.

If this does not solve the problem, you can check the chromosome names in your bigWig, by converting it to the uncompressed human readable format bedGraph using the tool UCSC Tools -> BigWig to bedGraph

Best,

Fidel

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Fidel Ramirez