Question: Paired End FASTQ files
gravatar for Mahesh.Hegde
5 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 • 296 views
ADD COMMENTlink modified 5 months ago by Jennifer Hillman Jackson23k • written 5 months ago by Mahesh.Hegde0
gravatar for Mo Heydarian
5 months ago by
Mo Heydarian790
United States
Mo Heydarian790 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 5 months ago by Mo Heydarian790
gravatar for Jennifer Hillman Jackson
5 months ago by
United States
Jennifer Hillman Jackson23k 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 5 months ago • written 5 months ago by Jennifer Hillman Jackson23k
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