How to combine multiple paired fastq files for quant

[James Lloyd]

Sorry if answered elsewhere but what if I wanted to combine multiple paired fastq libraries are the input to quant? For example if the same library was sequenced twice (technical replicates to be quantified as one) or just wanting to combine different samples into one super sample? Below is what code I think would work but if anyone has gotten this or an alt solution working, I would love to hear from you! 

./bin/salmon quant -i transcripts_index -l <LIBTYPE> -1 <(zcat reads_A_1.fastq.gz reads_B_1.fastq.gz reads_C_1.fastq.gz) -2 <(zcat reads_A_2.fastq.gz reads_B_2.fastq.gz reads_C_2.fastq.gz) -o transcripts_quant

- James

[Rob]

Hi James,

  The approach you describe here looks correct, and that's how I typically combine samples when I need to quantify them together.  The only extra trick I'd add is that, if you're using enough quantification threads, Salmon can actually process the reads faster than they can be decompressed.  Thus,

you might see a speedup if you replace `zcat` with `pigz -d -c -n <num_decompression_processes>` — this will do the same thing, but in parallel.

Best,

Rob