Question: Unifying RNAseq read length

Question

[moustafa_abohawya]

Hi All,

I'm trying to use different tools for detection of differential alternative splicing from RNAseq data, specifically MISO and rMATS. But both of them need RNAseq data with a defined read-length. Unfortunately, my data has a very wide range of read length from 50 to 185. I know that I should unify those length around the most occurrence read length which in my case is 140 bp reads in order to minimize information loss. So But I am not sure I know any tool that I can use to do that. I'd really appreciate if you know such tool to suggest them.

Thanks

Answer 1

[glihm]

Hi there,

You have a lot of options. ;)

The easiest way, if you are not well versed with command line and terminal is the Galaxy platform. Lots of tool for RNAseq are available.

EDIT : More precisely, the left column contains all tools. You can go to FASTA manipulation category, and you will see Filter sequence by length.

I hope that is helpful for you!

Answer 2

[Brian Bushnell]

With BBTools:

reformat.sh in=reads.fq out=filtered.fq ftr=139 minlen=140

[moustafa_abohawya]

Thanks for informing me about this tool, It sounds like a nice one.

I tried to use your command. But apparently it is output was almost trimmed like 52% of my input reads, which is like a huge percent of it has been trimmed

Is it a sign that I shouldn't filter based on read length?!

Do you have any suggestions?