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?