Separating concatenated fastq file into sample reads

Question

[María]

Hello all,

I concatenated all my samples into one file for doing transcriptome de-novo assembly (cat sample1.fastq, sample2.fastq, sample 3.fastq > all_samples.fastq).

I used Oyster River Protocol (ORP) to generate the transcriptome, and now I would like to do the quantification.

The issue comes because ORP applied Rcorrector to the concatenated read files (Forward and reverse) before assembling the transcriptome, and now I would need to separate the all_samples_Rcor.fastq into sample1_Rcor.fastq, sample2_Rcor.fastq and sample3_Rcor.fastq to accurately align my reads to the assembled transcriptome to do expression analyses.

Has anybody found this issue before? Cheers!