Question: Paired End FASTQ files
gravatar for Mahesh.Hegde
17 months ago by
Mahesh.Hegde0 wrote:

Hi all, I have a question regarding paired end FASTQ files for chip-seq analysis. Which following step is better to start with? 1) With FASTQ joiner to join 2 paired end FASTQ files or 2) Directly align in Bowtie2 using 2 different files? (also, in bowtie what is the best option for Do you want to set paired-end options ? Y/N)

Once I get the aligned files, in next step ( MACS2 callpeak option) what option I should pick? Are your inputs Paired-end BAM files? Y/N (as we have already made single file for paired end files, is it necessary to opt YES for this?).

I really appreciate your valuable answers, thank you.

alignment galaxy chip-seq • 1.6k views
ADD COMMENTlink modified 17 months ago by Jennifer Hillman Jackson25k • written 17 months ago by Mahesh.Hegde0
gravatar for Mo Heydarian
17 months ago by
Mo Heydarian830
United States
Mo Heydarian830 wrote:


If you have paired end reads you can go ahead and provide the "_1" and "_2" (or "F" and "R") pairs to Bowtie2. Typically you can use the default paired end options of Bowtie2, then modify these settings if the initial run produced poor mapping (or unexpected downstream results).

If you have paired end data, you should tell MACS2 that your data is paired end. The single output SAM/BAM of your Bowtie2 run will contain the information for the pairs of your reads.

Thanks for using Galaxy!


Mo Heydarian

ADD COMMENTlink written 17 months ago by Mo Heydarian830
gravatar for Jennifer Hillman Jackson
17 months ago by
United States
Jennifer Hillman Jackson25k wrote:


Input as two distinct datasets representing a pair, across the tools that use the fastq data. There are special data cases where some scientists do join (or assemble), but that is not how tools wrapped in Galaxy are expecting the input to be given and problems may come up.

Still, if interested, those alternatives are explained here. Reviewing will help you to decide how to proceed.

Tutorials for ChIP-seq analysis in Galaxy are available here:

Be sure to verify input format and datatype at the start of any analysis:

Thanks! Jen, Galaxy team

ADD COMMENTlink modified 17 months ago • written 17 months ago by Jennifer Hillman Jackson25k
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