How to combine my fq file based on sample

Question

[chiachoong_leong93]

Hello all,

Currently I have 4 main samples, each with 3 biological replicates for a total of 12 samples.

After running the sequencing, the raw data that I obtain in the fq file format was split, as an example

Sample A Biological Rep 1_1 Sample A Biological Rep 1_2 Sample A Biological Rep 2_1 Sample A Biological Rep 2_2 Sample A Biological Rep 3_1 Sample A Biological Rep 3_2

In total I have 24 files since all was split into 2 smaller files. Each file is about 15GB in size.

My aim is to combine all Sample A data together (which means combining all 6 files as explained above), how should I proceed?

Should I trim the adapters first before or after combining the data?

Eventually, I will combine Sample B, C and D and run differentially expressed gene analysis

I do have access to CLC Genomic Workbench if that will help.

Thank you!

Answer 1

[MatthewP]

Assumes it's paired-end sequencing and fastq files are in gzip format(xxx.fq.gz). You can merge fastq like:

zcat xxx_1_R1.fq.gz xxx_2_R1.fq.gz ... | gzip > xxx_R1.fq.gz

[Pierre Lindenbaum]

zcat+gzip. Don't . just use cat.