Question: How to prepare FastQ files for HISAT2
gravatar for skhan
16 days ago by
skhan30 wrote:

Hi there,

Should I be preparing or otherwise cleaning fastq files before I try to align them to a reference genome using HISAT2? If yes, how and using which tools?

I have 2x 76 bases paired end (separate R1 and R2 files) reads and am attempting RNA-Seq.


fastq alignment rna-seq hisat2 • 61 views
ADD COMMENTlink modified 15 days ago by Jennifer Hillman Jackson24k • written 16 days ago by skhan30
gravatar for Jennifer Hillman Jackson
15 days ago by
United States
Jennifer Hillman Jackson24k wrote:


Please see the Galaxy tutorials here:

Start with these:

  • NGS logistics - this is an introduction to Galaxy's functionality for the analysis of Next Generation Sequencing data.
  • RNA-seq: Introduction - an introductory tutorial for transcriptome analysis.
  • RNA-seq: Discovering and quantifying new transcripts - an in-depth transcriptome analysis example.

Thanks! Jen, Galaxy team

ADD COMMENTlink written 15 days ago by Jennifer Hillman Jackson24k
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