Read files for samples run across multiple lanes

[mellamosummer]

How do you recommend handling samples that have been run across multiple Illumina lanes?

For example, my read files are named like this:

sample1_L2_R1.fq.gz
sample1_L2_R2.fq.gz
sample1_L4_R1.fq.gz
sample1_L4_R2.fq.gz

[edgardomortiz]

Hi! You will need to concatenate them first:

cat sample1_L2_R1.fq.gz sample1_L4_R1.fq.gz > sample1_R1.fq.gz
cat sample1_L2_R2.fq.gz sample1_L4_R2.fq.gz > sample1_R2.fq.gz

You can do one by one or also use two bash loops if all your samples have the same naming pattern:

for file in *L2_R1.fq.gz; do cat ${file} ${file//_L2_/_L4_} > ${file//_L2/}; done
for file in *L2_R2.fq.gz; do cat ${file} ${file//_L2_/_L4_} > ${file//_L2/}; done

I hope this helps,

Edgardo