Which alignment mode to use?

foerstner-lab / READemption

A pipeline for the computational evaluation of RNA-Seq data

https://reademption.readthedocs.io

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Which alignment mode to use? #59

Closed termithorbor closed 8 months ago

termithorbor commented 8 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.

Tillsa commented 8 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.