I used two lanes on a flow cell for the same library. I have the fastq files now, and want to merge the data together for each duplicate sample. At what point of the downstream analysis should I merge the two, and what command do I use?
You can combine them with "cat". For example, if you have paired-end reads, you'll have 4 files, something like this:
You would combine them like this:
cat read1_L1.fq.gz read1_L2.fq.gz > read1_combined.fq.gz
cat read2_L1.fq.gz read2_L2.fq.gz > read2_combined.fq.gz
Do this as early as possible. If your sequences are single-ended then it's even easier.
I think you probably meant:
Good catch; edited :)
Thank you for your help!
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