BedGraphtoBigWig - UCSC

[Hparker]

Thank you for your replies.

Yes it should be sample_CO115, but I had used the code for something else.

I have used:

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

..but I get this error:

Error in write.table(sample_CO115, file = "sample_CO115.bedGraph", type = bedGraph, : unused arguments (type = bedGraph, seq = "\t")

[GenoMax]

Also "track type=bedGraph" declaration is minimally required for bedGraph files. Your file seems to lack that and would likely need to be added.

[Michael.Ante]

Hi Hparker,
you can modify your output from R:

write.table(mm2, file = "sample_CO115.bedGraph", [COLOR="Red"]row.names=F, col.names=F, quote=F, seq="\t"[/COLOR])

BTW, why do you call mm2? Shouldn't it be "sample_CO115"?
Cheers,
Michael

[Hparker]

I tired removing the column headings which is why now they are labelled as V1, V2...

[Hparker]

BedGraph file:

"V1" "V2" "V3" "V4"
"1" "chr11" " 104895" " 104895" "100.00000000"
"2" "chr11" " 123115" " 123115" " 0.00000000"
"3" "chr11" " 125931" " 125931" "100.00000000"
"4" "chr11" " 128336" " 128336" "100.00000000"
"5" "chr11" " 128338" " 128338" "100.00000000"
"6" "chr11" " 128379" " 128379" " 0.00000000"
"7" "chr11" " 128385" " 128385" "100.00000000"
"8" "chr11" " 128404" " 128404" "100.00000000"
"9" "chr11" " 128430" " 128430" "100.00000000"

[GenoMax]

BedGraph format files should look like: http://genome.ucsc.edu/goldenpath/help/bedgraph.html

Can you post 10 lines from your BedGraph file?

$ head -10 sample_CO115.bedGraph

[Hparker]

I am also using the bedGraphToBigWig tool: I am trying to create files I can upload to IGV to view the level of methylaiton. But when I carry out this command I get an error:

error: Expecting number field 2 line 1 of sample_CO115.bedGraph, got "start"

This is the code I used in R:

sample_CO115 <- read.table("sample_CO115.cov")
col <- c("chr", "start", "end", "meth_perc", "m", "u")
colnames(sample_CO115) <- col
sample_CO115$m <- NULL
sample_CO115$u <- NULL
write.table(mm2, file = "sample_CO115.bedGraph")

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

I removed the column headings but this did not work...

Please advise if you know how I can solve this!

[GenoMax]

Here is a simple guide to Mac Terminal (there are probably others): http://blog.teamtreehouse.com/introd...x-command-line

If you have not done this then that would be the first thing to do: http://seqanswers.com/forums/showthread.php?t=33389

Look at the second step to see how to run the program: http://www.biostars.org/p/42844/

[kayleighepps]

Hi

Would anybody be able to kindly provide step-by-step instructions for using the UCSC pre-compiled utilities such as the bedGraphtoBigWig tool? I am utilising Mac OS 10.9. I am not familiar much with terminal nor running such things and do not have any idea where to begin. Thank you very much!

- Kayleigh