Manipulating interleaved/interlaced fastq data

I upload SRR15324080 data in I am using Trimmomatic flexible read trimming tool for Illumina NGS data tool.

the data is paired end sequencing (merged in one file). So, I select paired end (as collection) in the tool but I do not see the name of my data in Select FASTQ dataset collection with R1/R2 pair. How can I set the default for this sample? Can anyone help me?

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Hi @m.esmaeilpour

The quickest way to import fastq data into Galaxy from NCBI with the pairs split is with the tool Faster Download and Extract Reads in FASTQ format from NCBI SRA. The output creates collections for you and can be used as input to Trimmomatic.

Or you can go back to the original interleaved reads and split them up – then run Trimmomatic on them. That particular tool might not fail on interleaved inputs but is also isn’t designed to handle them.

I added some tags to your post to help with how to split up the interleaved reads. And here is an FAQ and a tutorial that explain directly what interleaved fastq data is and how to manipulate it. Some tools accept that format, but most do not. But if you are trying to build up a workflow or plan to do a similar analysis again, using the tool that splits the read data at retrieval is simpler (and “faster”).



Hi again – it looks like you have tried to post this question a few times. It was on hold and is now approved. Please do not repeatedly post the same question or the system will block the Q&A.