BedGraphtoBigWig - UCSC

[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

[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/

[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]

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]

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"

[Hparker]

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

[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

[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.

[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")

[Michael.Ante]

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

[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")

[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]

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

[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]

Is your bedGraph file sorted?