Does Alignment Require All The Reads With The Same Length?

Question

[Tonyzeng]

HI, My question is as my title, also is that any tools to help me get the same length of reads?

Answer 1

[Ido Tamir]

It depends on the aligner, but the popular aligners I know (bowtie, bwa) don't require same length of reads (an early version of tophat required this). Maybe eland (CASAVA) with its hashing of reads requires the same length. For processing of reads there are many tools available e.g. http://hannonlab.cshl.edu/fastx_toolkit/commandline.html#fastx_trimmer_usage fastx trimmer

[Biomonika (Noolean)]

Also, if you feel uncomfortable using command line tool, you can trimm reads using online tools like galaxy http://galaxyproject.org/

Answer 2

[Tonyzeng]

Actually, I tried Galaxy to cut my overrepresent sequence, but my sequence is on 5' of read and reported as Illumina Single End PCR Primer 1. So I used Galaxy fastx-clipped but it can only clip adapt or primer sequence in 3'. So I changed to use cutadapt tool and cut 5' of read, it works well. However, I got a wide variety of length of reads after that from 0 bp to 88 bp

[Biomonika (Noolean)]

Galaxy can indeed do trimming from the 5'end. Just search more for the right tool.

[Josh Herr]

This is not an answer. Please add this clarification to your original question and delete this "answer". It will help us all keep track of how your question is answered. Thanks.

Answer 3

[Josh Herr]

If you're aligning your reads for phylogenetic analysis you'll have to have a matrix that is all the same length, so in that case, you'll have to trim. As Ido Tamir recommended, the FASTX TRIMMER from the Hannon Lab is very good.