[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]

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]

It includes chrM just not chrMT...

[GenoMax]

It includes chrM just not chrMT...

See my last post for an edit.

[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?

[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!

[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 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]

Show us the first 10 lines of your bedGraph file

$ head -10 sample_CO115.bedGraph

[Hparker]

type=bedGraphchr7 12784 12784 100
chr7 12948 12948 100
chr7 12962 12962 0
chr7 13071 13071 100
chr7 13107 13107 100
chr7 13119 13119 100
chr7 19750 19750 50
chr7 19751 19751 100
chr7 19771 19771 50
chr7 19772 19772 0

It appears to have type=bedGraph at the beginning of the file?

[GenoMax]

type=bedGraphchr7 12784 12784 100
chr7 12948 12948 100
chr7 12962 12962 0
chr7 13071 13071 100
chr7 13107 13107 100
chr7 13119 13119 100
chr7 19750 19750 50
chr7 19751 19751 100
chr7 19771 19771 50
chr7 19772 19772 0

It appears to have type=bedGraph at the beginning of the file?

Right but it has to be on a separate line by itself.

Edit so the file has a return:

type=bedGraph
chr7	12784	12784	100
chr7	12948	12948	100

[Hparker]

Ah great! Can you edit it manually? Or is there code?

[GenoMax]

You can edit manually (TextEdit or TextWrangler on Mac).

[Hparker]

Because I am now getting these errors:
Expecting at least 3 words line 1321892 of sample_CO115.bedGraph got 1

This is quite time consuming going through all the data to find where there are gaps.. is there a way of doing this in unix?

Thanks a lot for your help!

[GenoMax]

Is that the last line in your file (a blank line perhaps)?

$ wc -l sample_CO115.bedGraph