Forum: Bioinformatics
08-21-2013, 12:14 PM
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Replies: 0
Views: 1,053
Sicer questions
I am using Sicer to examine data from DNMT1 binding by ChIP-seq. I run IP and input and want to know
1) what is the ChIP island Read Count and Control island read count and how are they...
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Forum: Bioinformatics
03-28-2013, 10:32 AM
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Replies: 8
Views: 7,043
Thanks- I've tried that. I'm running MACS in a...
Thanks- I've tried that. I'm running MACS in a local Galaxy server which does not produce wig output files (MACS 1.4 in Galaxy). In addition this version of Galaxy does not allow us to view our...
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Forum: Bioinformatics
03-28-2013, 10:17 AM
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Replies: 8
Views: 7,043
How do you mean? Are you talking about the BAM...
How do you mean? Are you talking about the BAM file from Bowtie or the BED file from MACS? I find that the output from MACS is just a bar. On the other hand the BAM files are quite big and time out...
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Forum: Bioinformatics
10-24-2012, 01:03 PM
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Replies: 0
Views: 853
MACS score
In the absence of an input sequence to use as a control, does the MACS score have any meaning? I have two samples that I ran. I'm trying to understand if there is a way to understand something about...
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Forum: Bioinformatics
10-18-2012, 02:59 PM
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Replies: 0
Views: 960
Data normalization
I've noticed that many of the papers examining genome-wide ChIP use quantile-normalization. My impression was this was primarily for microarray types of data. It seems like normalization of ChIP-Seq...
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Forum: Bioinformatics
10-12-2012, 03:10 PM
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Replies: 0
Views: 1,079
New to MACS
I am running MACS14 within a University of Illinois Galaxy server and have some questions. How .wig files used over and above .bed files- if anyone has a good answer- I'd appreciate it.
1) Does...
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