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Question: Unifying RNAseq read length

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

rna-seq
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updated by Ram Ram • written by moustafa_abohawya • moustafa_abohawya

2 answers

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!

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updated by Ram Ram • written by glihm glihm

With BBTools:

reformat.sh in=reads.fq out=filtered.fq ftr=139 minlen=140
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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

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?

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updated by Ram Ram • written by moustafa_abohawya • moustafa_abohawya

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