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Forum: Bioinformatics 08-21-2013, 12:14 PM
Replies: 0
Views: 1,053
Posted By dgrayson
Question 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...
Forum: Bioinformatics 03-28-2013, 10:32 AM
Replies: 8
Views: 7,043
Posted By dgrayson
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...
Forum: Bioinformatics 03-28-2013, 10:17 AM
Replies: 8
Views: 7,043
Posted By dgrayson
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...
Forum: Bioinformatics 10-24-2012, 01:03 PM
Replies: 0
Views: 853
Posted By dgrayson
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...
Forum: Bioinformatics 10-18-2012, 02:59 PM
Replies: 0
Views: 960
Posted By dgrayson
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...
Forum: Bioinformatics 10-12-2012, 03:10 PM
Replies: 0
Views: 1,079
Posted By dgrayson
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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