MACS wig files on UCSC?

[yh253]

Dear all,

I got wig files for each chromosome from MACS peak calling output. Instead creating a custom tract for each chromosome, is there a way to join them into a single file and view it on UCSC genome browser? I googled around for a bit without success, it would be great if you could provide some help. Thanks!

[dawe]

Dear all,

I got wig files for each chromosome from MACS peak calling output. Instead creating a custom tract for each chromosome, is there a way to join them into a single file and view it on UCSC genome browser? I googled around for a bit without success, it would be great if you could provide some help. Thanks!

zcat *.wig.gz | wigToBigWig -clip stdin chromsizes.tab output.bigwig

[albireo]

Hi, I would also be interested in knowing how to do this. The above command fails with the following message:

Unrecognized line 7123307 of stdin:
track type=wiggle_0 name="[PATH]/[FILE]" description="Extended tag pileup from MACS version 1.4.2 20120305 for every 10 bp"

Thanks!

[dawe]

Hi, I would also be interested in knowing how to do this. The above command fails with the following message:

Unrecognized line 7123307 of stdin:
track type=wiggle_0 name="[PATH]/[FILE]" description="Extended tag pileup from MACS version 1.4.2 20120305 for every 10 bp"

Thanks!

You can try

zgrep -hv 'track' *.wig.gz | wigToBigWig -clip stdin chromsizes.tab output.bigwig

[howi]

Hi, I have the same problem. The -clip option did not help.

./wigToBigWig track1034.wig hg18.chrom.sizes track1034.bigwig
Unrecognized line 97361 of track1034.wig:
track type=wiggle_0 name="MACS_treat_chr13" description="Shifted Merged MACS tag counts for every 25 bp"

./wigToBigWig -clip track1034.wig hg18.chrom.sizes track1034.bigwig
Unrecognized line 97361 of track1034.wig:
track type=wiggle_0 name="MACS_treat_chr13" description="Shifted Merged MACS tag counts for every 25 bp"

[health1987]

The -S option will works.