Paired-end Illumina data

[hoelzer]

Is it possible to also use the pipeline w/ paired-end data? Thanks!

[rvalieris]

it should just work, I'm using paired-end data as well, it should look like this:

$ ls data/fastq/
sample1_1.fastq.gz
sample1_2.fastq.gz
sample2_1.fastq.gz
sample2_2.fastq.gz
[....]

[hoelzer]

He @rvalieris thanks! But then, the paired-end reads are not mapped and analyzed together but separately, or? Or can I write in the tags_pool_mypool file something like:

sc2-mix

when I have in data/fastq

sc2-mix.R1.fastq.gz
sc2-mix.R2.fastq.gz

?

[hoelzer]

Ah, I see here

https://github.com/rvalieris/LCS/blob/master/rules/pools-pipe.py#L13

that the files must be likely named like you already mentioned, so in my case

sc2-mix_1.fastq.gz
sc2-mix_2.fastq.gz

and then in the tags_pool_mypool:

sc2-mix

I guess

[hoelzer]

Alright yes, that seems to work.

[rvalieris]

thats correct ! the filename pattern is important for the pipeline to pick it the pairs.