Question: Can Soap2 Be Used For Rna-Seq Analysis
gravatar for Wligtenberg
8.1 years ago by
Wligtenberg10 wrote:


I want to re-analyse results of RNA-seq data. Previously, they have been analysed using SOAP2 and an old reference genome. When I contacted the author of snpEff (because I want to check the SNP effects later on) he mentioned that he was unsure if SOAP2 could be used to analyse RNA-seq data, because it can't map across exon boundaries. So, can SOAP2 be used for RNA-seq mapping or not? Or can it be used, but does another tool (like TopHat) a really better job?

Thanks in advance.

short aligner rna • 2.2k views
ADD COMMENTlink modified 8.1 years ago by Malachi Griffith18k • written 8.1 years ago by Wligtenberg10
gravatar for Malachi Griffith
8.1 years ago by
Washington University School of Medicine, St. Louis, USA
Malachi Griffith18k wrote:

If you want to align RNA-seq reads with an aligner designed for DNA mapping you can create a custom reference genome that contains the chromosomes plus a database of exon-exon junctions. This deals with the issue of mapping reads across exon-exon junctions, but it limits your detection to those junctions that you define in your database. Several groups have used this approach to align RNA-seq reads with BWA and other aligners that are not 'splice-aware'. If your reads are long (>75 bp), the simplest solution is probably just to use TopHat to align your reads against a standard reference genome. It will definitely do a better job than simply using SOAP2 against the standard reference genome. In addition to TopHat there are many other 'splice-aware' aligners designed with RNA-seq reads in mind. These include: TopHat, SpliceMap, MapSplice, hmmSplicer, Supersplat, SOAPsplice, etc.

Of course there are also many other older splice aware aligners that would produce useful results but are too slow to be practical when aligning the number of reads typical in an RNA-seq experiment. These include: BLAT, Exonerate, Spidey, Splign, etc. They might still be useful in the context of performing an evaluation of the next-gen splice-aware aligners with a test data set.

ADD COMMENTlink modified 8.1 years ago • written 8.1 years ago by Malachi Griffith18k

So, in short. Using SOAP2 with a standard reference genome is not a good idea, right?

ADD REPLYlink written 8.1 years ago by Wligtenberg10

Right, not a good idea. Not for RNA-seq in any case.

ADD REPLYlink written 8.1 years ago by Malachi Griffith18k
gravatar for Istvan Albert
8.1 years ago by
Istvan Albert ♦♦ 81k
University Park, USA
Istvan Albert ♦♦ 81k wrote:

In general one cannot take a tool designed for DNA mapping and directly use it for transcriptome data unless the data has certain characteristics or the questions that need to be answered are very simple.

You will need to find a tool that can handle the job. Note that the tasks may be quite challenging as shown for example in Transcript assembly and quantification by RNA-Seq... (Nature Biotechnology, 2010)

ADD COMMENTlink written 8.1 years ago by Istvan Albert ♦♦ 81k
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