search

foerstner-lab / READemption

A pipeline for the computational evaluation of RNA-Seq data
https://reademption.readthedocs.io
Other
36 stars 19 forks source link

Which alignment mode to use? #59

Closed termithorbor closed 3 months ago

termithorbor commented 3 months ago

Hi, I have sequenced reads with Illumina 2 x150 bp: However, I am not sure if all reads can be merged since I have also In my library which are bigger than 300 bp (see profile below). Is it still useful to run --paired_end mode or what is the best way to run the alignment?

Thanks in advance.

image

Tillsa commented 3 months ago

If you have paired end reads you should use the option --paired_end. Per default, READemption will merge the two reads of a pair to represent the originating template and save the resulting alignment of the entire template represented as a single read. If you do not want to merge the reads of a read pair you can turn that off by using the option --no_fragment_building.