Tools For Large Indels Discovery In Single-End Rna-Seq Reads

Question

[Axel Kuehn]

Hi all,

Has anyone heard about any tool wich could deal with large indels discovery? I've found some for paired-end reads but never for single-end... My final goal is to find transposable elements polymorphisms in these RNA-seq reads.

Thanks in advance!

Answer 1

[lh3]

No, there is no such tool for your purpose. Probably you have to use multiple mappers to do several rounds of alignments. You may use TopHat etc to get normally spliced reads, use a local aligner (BLAT/BLAST/BWASW) to find partial hits, and then write your own script to get the ME insertion.

Watch out that it will be very tricky and error-prone for RNA-seq reads.

[Axel Kuehn]

Ok! thank you by the way, so I think I will try a more standard way to find out my differentially expressed TE's...

Answer 2

[Michael]

Are you looking for an aligner? Look at blat or SSHA2, or lastz, I know, they are not specifically 'short-read' or 'NGS' aligners and might be substantially slower than bwa or bowtie. However, they perform well with insertions/ deletions, and I found that the sensitivity might be better than with most 'short-read' aligners, given larger indels.

[Axel Kuehn]

Sorry, I might missed some informations on what I've done : I've still aligned my fastq files with tophat and therefore got corresponding BAM files. However your approach seems interesting in an indel point of view but I'm afraid of the run time! (~7GB files)

Answer 3

[Sean Davis]

I do not know exactly what you mean by "large indels", but you could take a look at GSNAP which is an indel-aware and RNA-seq capable alignment algorithm.

[Axel Kuehn]

OK, I'll give it a try!