fastp output files

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I am new to NGS. I used FastP for preprocessing and now want to proceed with HISAT2 for alignment. I’m a bit confused about the output files:

  1. What do the ‘Read 1’ and ‘Read 2’ output files from FastP represent?
  2. My FastP output is labeled as ‘FastP on data 1 and 2,’ but it includes a ‘Read 1’ file—why is that?
  3. Which files should be used as input #1 and input #2 in HISAT2?"
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Hi @Krutika_Sadadekar

If you scroll down to the bottom of a tool form, in the latter part of the Help section with the summary help, you’ll find links to any tutorials that include that tool. These tutorials are for training – so include technical help but also scientific help linked to those technical choices – these should be helpful.

In that same tutorial area where the Quality tutorial was located are two more tutorials that will interest you.

This one explains more about common data formats used in NGS analysis - including fastq and bam and a few others. It will help you to match together common data labels with the data inside a file itself. Read 1 and Read 2 mean something very specific: which end of a read pair the data inside the files represents. Super important!

Then you can proceed to the Mapping tutorial here to learn how to map, and you’ll understand your input (fastq data) and the output (BAM) content more plus can refer back to the first guide if something comes up (maybe a tool form option seems unclear). You can also ask questions here.

We have a Learning Pathway you could explore since you are now several steps in. If interested, please see:

Hope this helps!