From: "Moreau, Morgane" <morgane.moreau@jcu.edu.au>
Date: Tue, Oct 27, 2015 at 2:45 AM
Subject: Re: Chip-seq in galaxy
To: Freese, Nowlan <nfreese@uncc.edu>

Dear Ms Freese,

I followed the video tutorial on Chip-seq analysis and visualization on Galaxy.

I am mapping my reads to the E. coli genome, custom build, in a galaxy instance (GVL-QLD)

I have two problems I was hoping you could help me with.

First when I map with Bowtie I end up with a SAM file in which some rows have the sequence in the qual score columns and the qual score in the OPT column. While other rows are fine. ) I didn’t manage to fix that so I mapped my reads with BWA. After removing the unmapped reads I tried pick calling with MACS and it keeps failing.

I have 70,000 sequence in my treatment sample and 150,000 in my control (input).

I get this error message:

INFO @ Tue, 27 Oct 2015 17:28:06:

1. ARGUMENTS LIST:

1. name = MACS_in_Galaxy

1. format = SAM

1. ChIP-seq file = /mnt/galaxy/files/000/117/dataset_117750.dat

1. control file = /mnt/galaxy/files/000/117/dataset_117749.dat

1. effective genome size = 4.00e+06

#

And that one in the generation errors:

WARNING @ Tue, 27 Oct 2015 17:28:10: Too few paired peaks (0) so I can not build the model! Lower your MFOLD parameter may erase this error.

WARNING @ Tue, 27 Oct 2015 17:28:10: Process is terminated!