pipeline for single end

[sebapoljak]

Dear Eric Normandeau,

We would like to run the pipeline only with the R1 sequences (single end read), Is it possible? How? Thank you

[enormandeau]

Hi. Do the forward sequences contain both of the primer sequences? If yes, we could cheat the pipeline to use those. If not, I guess we could add them and then cheat barque the same way.

Could you please send me a small dataset (maybe only 1000 reads for 4 samples) so I can test things and potentially write a script to prepare the data? I would also need the sequence of the primers.

[sebapoljak]

Thank you for your response.
The forward sequence contain only the forward primer sequences (MFish Forward).
Here I send you 4 samples. Thank you in advanced!
mifish-c3_S40_L001_R1_001.fastq.gz
mifish-rem1_S36_L001_R1_001.fastq.gz
mifish-rem2_S37_L001_R1_001.fastq.gz
mifish-2ma_S34_L001_R1_001.fastq.gz