QuEST ChIP-seq group

There is nothing special about ATAC-seq that would require a different analytical pipeline that is

Hello, I am very new to chip-seq data. I have run bowite with my illumine reads on remote server. Now

Hi all, I've been trying to run QuEST. I am working on a sponge species I have thousands of

Hi all, I've been trying to run QuEST. I am working on a sponge species I have thousands of

Hi Liang, when you see the peaks, is it by uploading wig files from QuEST? Try repeating analysis

I posted the answer to a different thread. You can post there if you have more questions. Thanks,

Hi Anton, When I rebuilt the genome table by replacing the \t with a space, it works now. Thanks,

Hello QuEST Group, I uploaded ChIP_normalized_wig file into UCSC genome browser to show peaks.

Hi Xin, I've seen this error before, but I didn't have enough info from the user to tell what

Hi Ruidong, you can provide a path to a directory containing individual fasta files with chromosomes

Hi Theodore, thank you for your patience. It seems I found a small bug in genome table generation,

Hi Anton, Thank you very much for the reply. This is all I need. Best, Antonio On Apr 14, 2014 2:10

See my response to another thread. On Friday, April 11, 2014 8:16:57 AM UTC-7, Theodore Georgomanolis

Hi Tim, the number of peaks does not strongly depend on the peak shift for small values of peak shift

Are you using the latest QuEST version 2.4? You can grab it here: http://www-hsc.usc.edu/~valouev/

To see the first 10 lines try this: head -10 yourfile.bed To count the number of lines wc -l yourfile

There is a bed file for the peak positions and another bed file for the region positions. See the

$ sed 's/chr=1/chr=chr1/g' file-in > file-out "s" means substitute The string in

Yeah, the 30GB swap I would up using was enough, but it was slow; it took about 30 minutes just to

Does it accept your files though? QuEST prints the progress while parsing your input files and you

Hi Emma, yes, it is possible. Check out the QuEST tutorial. QuEST provides normalized wig score files

KL, this may indeed be a bug of some sort. Can you share with me (in an email) a QuEST file with

http://www-hsc.usc.edu/~valouev/QuEST/QuEST.html On Wednesday, August 29, 2012 12:18:45 AM UTC-7, anu

Bowtie format is no longer supported. It might have changed since last time I looked at it. The best

I'm using QuEST to analyze our lab's chIP-seq data and comparing it with the analysis done by

Yes, you can exit after configuration script and edit those files. Then run run_QuEST_with_param_file

Hi Kushal, not an expert on Bowtie unfortunately. Perhaps refer to their manual to determine how to

Hi Anton, It was a disk-space issue. I only had a few hundred GBs left on the disk. I added another

thanks for the reply i will waste no more time. earlier i used samtools-0.1.7a/misc/export2sam.pl to

Thanks, these are warnings, not a big deal. In regard to your earlier question - you do not need to