Split DNA sequences from 150pb to 75 pb

Question

[Ismael]

Hi there!

I have perform a NovaSeq 6000 run with two pools. One of them was WES and the other with RNA-Seq data, both was 2x150 bp reading. The recommended parameters for RNA-Seq is 2x75 bp, so I want to split my RNA-Seq data from 2x150 bp. Anyone know if is it possible to perform that cut? And if it is, how could I do it?

Thanks!!

[Ismael]

Thank you for all your responses!! I have finnally decided to continue with my long-read data.

Answer 1

[lieven.sterck]

there does not exist something as 'the recommended parameters for RNA-Seq' , so do not worry about it.

the only important parameter is what your experiment/analysis is like (or what you hope to get out this experiment)

Just leave them as they are and run your analysis with the complete set/read length. I fear your will hinder the downstream analysis more than that you will improve it by starting to fiddle with your input data

Answer 2

[ATpoint]

Don't do that, the longer the reads the better for RNA-seq as greater length makes alignment more reliable. Continue with the data as-is.

Answer 3

[GenoMax]

If you do need to trim the data down (which may be needed if you have pre-existing data that was sequenced at 75 bp and you want to do a comparative analysis) then you can use reformat.sh from BBMap suite.

reformat.sh -Xmx4g in=input.fastq.gz out=trimmed.fastq.gz forcetrimright=75 (# for single end reads)

reformat.sh -Xmx4g in1=R1.fastq.gz in2=R2.fastq.gz out1=R1_trim.fastq.gz out2=R2_trim.fastq.gz forcetrimright=75 (# for paired-end reads)

If this does not apply then you already have recommendations from others to continue as is.