Question: Can someone give me a foolproof instruction on how to merge R1 and R2 illumina fastq files
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3.2 years ago by
shuo.li10 wrote:

Dear Galaxy experts,








I need to merge R1 and R2 Illumina paired end reads. The amplicon was ~550nt, sequenced using 300nt x2 Illumina chemistry. The 2 reads should overlap in middle. so it is an align/merge task. 

After loading the data to Galaxy, I could not figure out what to do next. Can someone please give me a foolproof instruction, or step by step which button to press, for this task?

With many thanks, Lucy










lay instructions • 1.0k views
ADD COMMENTlink modified 3.2 years ago by Jennifer Hillman Jackson25k • written 3.2 years ago by shuo.li10
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3.2 years ago by
United States
Jennifer Hillman Jackson25k wrote:


The Fastq dataset merging tool in Galaxy do not address overlap resolution. This are a straightforward merge: end-to-end.

If there a reason why you want to do this at the start of the experiment? The NGS mapping tools wrapped for Galaxy and available on the public Main server at are designed to work with pair-end reads given as individual dataset inputs. There are both technical and scientific reasons why this is desirable. 

Please share more about what you are trying to accomplish downstream (perhaps include target tools or workflows) if this does not help. If the question is broad and involves many details, please start up a new post. You can always link this one in for reference. One question per-post is the best way to organize information at this support forum.

Just for reference, please see the Learn/GalaxyNGS101 for the most common workflow procedures utilizing the tool sets hosted on There are many other tools and pipelines (sourced from the Tool Shed for a local/cloud Galaxy and/or hosted-executed on other public Galaxy servers with domain focus), but guessing which is applicable for your research isn't the best way to help you move forward with your analysis goals. 

Thanks! Jen, Galaxy team

ADD COMMENTlink written 3.2 years ago by Jennifer Hillman Jackson25k

Thank you very much for the helpful explanation.

I have another question: after quality filter some reads become considerable shorter. If I want to filter out all reads <50nt, or keep all the reads > 50nt, for a fastq file, how to do this?

Thanks a lot for your help

Shuo Li

ADD REPLYlink written 3.2 years ago by shuo.li10
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