Re: [galaxy-user] Adding a custom genome for using MACS in Galaxy

Thanks Jen for a detailed explanation. One question I have is- If I run the MACS on my pre-aligned  reads on ChIPseq data, will I be be able to annotate my peaks from MACS either using  fetch to  closet non-overlapping feature or profile annotation. In summary is there a way to annotate peaks fo

[galaxy-user] Fwd: Galaxy: RNA-seq analysis problems

Roberta, I'm traveling right now so I'm forwarding your message to our help list. Thanks. -- Forwarded message -- From: Roberta Galletti Date: Tue, Sep 11, 2012 at 5:19 AM Subject: Re: Galaxy: RNA-seq analysis problems To: James Taylor Hello James, sorry to bother you again, bu

[galaxy-user] MACS out put files from Galaxy

I ran MACS on my chipseq dataset and found various files: 1. under html report there ar etwo files one of negative peaks.xls and second is peaks.xls the file peaks.xls is same as peaks .intreval file in the right out put flow with one bp position added e..g if peak coordinate under html report ar

Re: [galaxy-user] MACS out put files from Galaxy

Hi Peter, I will try to give you my basic understanding of how MACS works. But before, I would recommend you to read the MACS Readme , where you will find detailed explanations of how MACS works and what the different output files are. 1.

Re: [galaxy-user] interupted running jobs restart

On Aug 27, 2012, at 8:53 AM, petr wrote: > We are running galaxy on pbs cluster. In out setting some jobs can take > several weeks to finish and it is virtually impossible to wait for suitable > moment when server can be restarted or turn down without interrupting > running tasks. Is there an opti

Re: [galaxy-user] MACS out put files from Galaxy

Hi Peter, Florian's answers are very good - I am not sure this will add much, but perhaps a little, for the Galaxy output datasets parts of the questions ... The latest Using Galaxy paper, protocol 3, includes all of the "optional" output that MACS in Galaxy will produce (in addition to the

[galaxy-user] Peak-calling with MACS from .bowtie file

Hi, I have ChIP-seq alignment files in .bowtie format and would like to perform peak-calling using MACS. However, .bowtie format doesn't seem to be supported in Galaxy. Is there a way around to have MACS analyze these files within Galaxy, or is the only option to use MACS in command line? Thank y