Assign libraries for paired end data in the reademption deseq command

[termithorbor]

Hi,

how do I assign the libraries for paired end data in the reademption deseq command?

The names of my reads are like this:

1-hour-1A_p1.fq
1-hour-1A_p2.fq
1-hour-2A_p1.fq
1-hour-2A_p2.fq

Where p1 are the forward and p2 the reverse reads.

Do I have to wirte:
a) --libs 1-hour-1A,1-hour-2A
or
b) --libs 1-hour-1A_p1.fq,1-hour-1A_p2.fq,1-hour-2A_p1.fq,1-hour-2A_p2.fq

I would assume a) but a statement in the manual would be very helpful since the examples are solely for single end data.

Thanks in advance,
Thorben

[Tillsa]

Hello @termithorbor

It is option a)

And thank you for pointing out that the documentation is missing a paired end data example, we will fix this.

Best,
Till