When to merge multiple fastq files into one for RNAseq analysis?

When to merge multiple fastq files into one for RNAseq analysis?

1

I’m a little confused on the files I am trying to analyze and so I just wanted to doublecheck on here before proceeding if that’s okay:

For each RNA-seq sample (paired end sequencing), the sequencing core gave back 4 fastq files: samplenameL001_R1, samplenameL001_R2, samplenameL002_R1, samplenameL002_R2. Are the L001 and L002 separate replicates, or are they separate pieces of the same sample?

If the latter, I was thinking of combining the two fastq files (so combining the R1s together and the R2s together) before trimming them for adapters/quality. Would this be the correct thing to do? Or should I trim them all separately and combine them like so before using bowtie2 for aligning?

Or am I going about this totally wrong and if so, should I just stick to aligning them separately?

Thank you!


rnaseq


aligning


bowtie2

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