Question: The best aligner to align RNA-Seq data into mitochondria genome
1
gravatar for zxzhao5
3.9 years ago by
zxzhao510
United States
zxzhao510 wrote:

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.

 

mitochondria rna-seq latest • 1.7k views
ADD COMMENTlink modified 3.9 years ago by Nicolas Rosewick8.3k • written 3.9 years ago by zxzhao510
1
gravatar for Nicolas Rosewick
3.9 years ago by
Belgium, Brussels
Nicolas Rosewick8.3k wrote:

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

ADD COMMENTlink written 3.9 years ago by Nicolas Rosewick8.3k

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.

ADD REPLYlink written 3.9 years ago by Devon Ryan92k

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

ADD REPLYlink written 3.9 years ago by Nicolas Rosewick8.3k

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.

ADD REPLYlink modified 3.9 years ago • written 3.9 years ago by michael.ante3.4k

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

ADD REPLYlink written 3.9 years ago by Devon Ryan92k
0
gravatar for Devon Ryan
3.9 years ago by
Devon Ryan92k
Freiburg, Germany
Devon Ryan92k wrote:

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!

ADD COMMENTlink modified 3.9 years ago • written 3.9 years ago by Devon Ryan92k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 912 users visited in the last hour