FastQC for paired end data
Hi, I have 36 fastq files of paired end RNA-seq so I was wondering if anyone knows how to do fastqc on paired-end data? and what is the difference between fastqc of single end data? I have done with single end data before but never with paired end so please help me. Thank you!
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MarkiMark •
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Dk •
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Dk •
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you can do:
fastqc dir/of/files/sampleX_1.fastq.gz --outdir=/data/resfolder
fastqc dir/of/files/sampleX_2.fastq.gz --outdir=/data/resfolder
and put it in a loop if you don't want to do it manually for all files..
@liorglic mentioned MultiQC which is simpler to run
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fastqc works with single files only. Do fastqc on all files and summarise multiple fastqc outputs with multiqc. Fastqc provides QC data as tsvs and you can parse them as per your requirements.