multiqc hisat2 question

Question

[smithkthedale]

I have my cutadapt.fastq.bz2 files, sam files, bam files, and sorted.bam files all in a folder called outputArabidopsis. I want to turn my cutadapt and hisat2 results into a multiqc report. How do I do so? What is the command.

I know it's multiqc . but when I do this, only one sample appears on my multiqc desktop. I want a report with all my cutadapt and hisat 2 data in the same browser.

Are my hisat2 results in the sam/bam/or sorted file?

What is the command to put my cutadapt and hisat 2 results into multiqc?

Answer 1

[Phil Ewels]

You can find details of how MultiQC finds outputs in the documentation. For example, HiSAT is here and is as follows:

kallisto:
  contents: '[quant] finding pseudoalignments for the reads'
  shared: true

As the docs say, the easiest way to get the output you need from HiSAT2 is to use the --new-summary flag when you run it. Otherwise, capture the standard out / standard error to a file and MultiQC should find that.

Cutadapt is similar (docs) and also typically works with capturing standard out to a file. For example:

$ cutadapt mysample.fastq.gz > logfile.txt

I hope this helps!