I have the following samples:
I would like to align these fastq files to the reference library. Bowtie2 is the tool I am using. As you can see, the same sample was spread across 2 lanes in order to obtain adequate sequencing depth. The expected output is a count matrix that will be further analysed using DESeq2.
How (and when) to proper treat and merge the same sample from two different lanes?
Are they technical replicates? If not, you can merge them before mapping with the simple cat command.
They are not. The shown samples are from the same multiplex, and the multiplex was then sequenced on 2 lanes. What are you suggesting is to merge them before the alignment? R1.fastq from both lanes and same for R2.fastq?
Yes, merge all forward and reverse read files separately.
If they same from the same library prep, they absolutely are technical replicates, no matter how many different lanes they are split over.
Thanks a lot for your suggestion!