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Old 12-09-2010, 05:27 AM   #1
yh253
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Default MACS wig files on UCSC?

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!
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Old 12-09-2010, 11:23 AM   #2
dawe
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Quote:
Originally Posted by yh253 View Post
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!
Code:
zcat *.wig.gz | wigToBigWig -clip stdin chromsizes.tab output.bigwig
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Old 11-26-2012, 01:05 PM   #3
albireo
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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!
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Old 11-26-2012, 11:29 PM   #4
dawe
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Quote:
Originally Posted by albireo View Post
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

Code:
zgrep -hv 'track' *.wig.gz | wigToBigWig -clip stdin chromsizes.tab output.bigwig
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Old 11-27-2012, 11:38 PM   #5
howi
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Hi, I have the same problem. The -clip option did not help.

Quote:
./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"
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Old 08-30-2013, 02:13 AM   #6
health1987
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The -S option will works.
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