Question: Analysis of forward and reverse reads
gravatar for joseph.andrews
17 months ago by
joseph.andrews20 wrote:


Newbie here: I have recently done some chip-seq, and for each sample, I have different FASTQ files for forward and reverse reads (forward and reverse reads differentiated by -1 and -2 file extensions, respectively). There are a total of 12 samples. My question is: how do I deal with this. Do I want to combine the -1 and -2 (forward and reverse reads) for each sample, or keep them separate. Also, each of the 12 samples were run on 4 lanes, so I actually have 4 forward and 4 reverse reads for each sample. These I WILL combine before alignment.

Any suggestions would be welcome

analysis chip-seq • 728 views
ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson25k • written 17 months ago by joseph.andrews20
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Combine the paired-end data into a dataset collection then use the collection as the input to analysis tools.

Tutorials for ChIP-seq analysis are here:

A Dataset Collection can be used along with a Workflow to do the analysis. Help for using collections and workflows are also in the link above. The tool Concatenate can be used to merge the fastq data into samples before building the input collection datasets. Use the "list of pairs" data collection type (forward reads are grouped into a list, reverse reads are grouped into a list - all in one step - and those are input to tools). To further manipulate the collection data, see the tools in the group Collection Operations.

Hopefully, this helps! Jen, Galaxy team

ADD COMMENTlink written 17 months ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 183 users visited in the last hour