[GenoMax]

Show us the first 10 lines of your bedGraph file

$ head -10 sample_CO115.bedGraph

[Hparker]

I am still having the problem with creating the bigWigs - this is the error I get:

type=bedGraphchr7 is not found in chromosome sizes file

[GenoMax]

I used the following to try and replace chrM with chrMT but it did not work:
sed 's/chrM/chrMT/' hg19.chrom.sizes

is there a better alternative?

Do this

$ sed --in-place=.bak s'/chrM/chrMT/' hg19.chrom.sizes

This will edit the file and make a backup copy (.bak) at the same time. Let us see if this fixes the error.

[Hparker]

I don't understand what is wrong with the chromsizes file

$ wget http://hgdownload.cse.ucsc.edu/admin...etchChromSizes
$ chmod 777 fetchChromSizes
$ ./fetchChromSizes hg19 > hg19.chrom.sizes

I again got an error, but this time with chr7:

type=bedGraphchr7 is not found in chromosome sizes file

Please help!

[Hparker]

I used the following to try and replace chrM with chrMT but it did not work:
sed 's/chrM/chrMT/' hg19.chrom.sizes

is there a better alternative?

[GenoMax]

It includes chrM just not chrMT...

See my last post for an edit.

[Hparker]

It includes chrM just not chrMT...

[GenoMax]

If you posted the entire contents of the chrom.sizes file above then it does not seem to contain chrMT.

Edit: I think the discrepancy is in the name. Your file probably has chrMT, where as the chrom.sizes file refers to chrM. UCSC likely will expect chrM so you could edit that in your own file. If you don't care about chrM data then you could edit the chrom.sizes file (that data will then not display).

[Hparker]

I have now sorted using:

$ sort -k1,1 -k2,2n sample_RB49.bedGraph > sample_RB49_sorted.bedGraph

and it now says:
chrMT is not found in chromosome sizes file

[GenoMax]

Is your bedGraph file sorted?

[Hparker]

chr1 249250621
chr2 243199373
chr3 198022430
chr4 191154276
chr5 180915260
chr6 171115067
chr7 159138663
chrX 155270560
chr8 146364022
chr9 141213431
chr10 135534747
chr11 135006516
chr12 133851895
chr13 115169878
chr14 107349540
chr15 102531392
chr16 90354753
chr17 81195210
chr18 78077248
chr20 63025520
chrY 59373566
chr19 59128983
chr22 51304566
chr21 48129895
chr6_ssto_hap7 4928567
chr6_mcf_hap5 4833398
chr6_cox_hap2 4795371
chr6_mann_hap4 4683263
chr6_apd_hap1 4622290

[GenoMax]

Can you show us what hg19.chrom.sizes contains?

[Hparker]

Thank you both for your answers. I managed to write to a bedGraph file however when I now convert to a bigWig:

$ bedGraphToBigWig sample_CO115.bedGraph hg19.chrom.sizes CO115.bw

I get the following error:
type=bedGraphchr7 is not found in chromosome sizes file

I downloaded the chrom.sizes file using the following code:

$ wget http://hgdownload.cse.ucsc.edu/admin...etchChromSizes
$ chmod 777 fetchChromSizes
$ ./fetchChromSizes hg19 > hg19.chrom.sizes

[GenoMax]

There was a typo in @Michael.Ante's code

write.table(sample_CO115, file = "sample_CO115.bedGraph", row.names=F, col.names=F, quote=F, sep="\t")

Add the "type=bedGraph" line afterwards along with any additional lines (e.g. browser intervals etc) using an editor.

or you could do this

cat('track type=bedGraph\n', file='sample_CO115.bedGraph', append=F)
write.table(sample_CO115, file = "sample_CO115.bedGraph", append=T, row.names=F, col.names=F, quote=F, sep="\t")

[Michael.Ante]

Sorry, it has to be sep="\t" (for field-separator).