Macs 1.4 Fail To Output File.R And File.Wig

Question

[Dsoronellas]

That's the question:

When I tun MACS ver. 1.4 I don't get as output the file.R and the file.wig. How can obtain those files?

This is de command I use:

macs14 -t file.map --format=BOWTIE --name=EXPERIMENT --pvalue=1e-3 --bw=80 --tsize=36 --nomodel --shiftsize=80 --call-subpeaks --wig

And obtain:

1.- compressed wig files in a folder

2.- file.peaks.bed

3.- file.summit.bed

4.- file.peaks.xls

[KCC]

Can you give some more detail. Does the command fail to produce any output at all?

Answer 1

[Sukhi Singh]

You should paste your error log here for a quick answer in future. So, file.R is an R script which you can use to produce a PDF image about the model based on your data. You are using --nomodel parameter which will bypass the model building thus the file.R wont be produced. Secondly, for the file.wig, you have to merge all the wig files produced for each chromosome for your data into a single wig or a better bigwig file. The wig are present in the folder which is produced along with the other files you mentioned there. Most likely the folder name will be like EXPERIMENT_MACS_wiggle, enter it and a subfolder called treat and there launch this command zcat *treat*.wig.gz | grep -v ^track | wigToBigWig -clip stdin mm9.chrom output.bw, for this you need to install the ucsc utility wigToBigWig and chromosome size, grab it from here http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/

Cheers