The best aligner to align RNA-Seq data into mitochondria genome

Question

[zxzhao5]

Hello all:

I am working on the RNA-Seq project on non-model organism. The genome is not available for this organism but the mitochondria has been sequenced and published.

I want to remove all mt sequence from my original fastq files so I am going to align my reads (100bp pair-end) to mt genome. I want to use Bowtie 2. But I found Bowtie 2 is designed for "quickly aligning large sets of short DNA sequences (reads) to large genomes".

The animal mt genome is relatively small so I am wondering if Bowtie 2 still work? I want to use this because one of its output option is unmapped reads, which is exactly what I want.

Answer 1

[Nicolas Rosewick]

If it's RNA-Seq you should use a splice-aware aligner e.g. STAR, Tophat, ...

[Devon Ryan]

I totally missed the RNAseq part of this :(

One caveat about STAR is that you have to tweak setting to map against small genomes. I'm think this is mentioned in the documentation, but I saw a thread about this on SEQanswers this week so apparently this isn't quite documented well enough.

[Nicolas Rosewick]

Generally, --genomeSAindexNbases needs to be scaled with the genome length, as ~min(14,log2(ReferenceLength)/2 - 1) at the genome index generation step.

[michael.ante]

A stupid question, but is there any splicing in the Mitochondria? Since it's more or less still a procaryote and the annotations I know don't include any junctions.

[Devon Ryan]

I happened to look this up and at least in some organisms the answer appears to be "yes, there's splicing".

Answer 2

[Devon Ryan]

Yeah, it'll still work fine. The test data set that comes with bowtie2 is from a phage lambda, whose genome is ~49kb (so not that much larger than a mitochondria).

Edit: D'OH, I missed that this is RNAseq! Follow NicoBxl 's advise!