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iontorrent RNAseq alignment

What aligner may be best for ion torrent RNA-seq data; I generally use for illumina TopHat. Any pointers please.

rna-seq
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written by kanwarjag kanwarjag

I suggest you try BBMap, as it is capable of handling both splice junctions and the Ion Torrent's indel-containing error profile. Are you aligning to a genome or transcriptome, and what species?

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written by Brian Bushnell Brian Bushnell

I am aligning to hg19 genome. That mean we cannot use TopHat for ion torrent. I could not find exact paper but I remember they have used top Hat and unaligned reads were realigned with Bowtie2 both TopHat and Bowtie2 alignments combined and used for differential analysis. Any thoughts. Otherwise I can turn to BBMap

Thanks

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written by kanwarjag kanwarjag

You can try TopHat + Bowtie2, or just TopHat alone. They should work, but I would expect BBMap to be faster and do a better job. For human genome RNA-seq alignment I recommend adding the flags "maxindel=100k intronlen=10".

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written by Brian Bushnell Brian Bushnell

Hello kanwarjag,

Could you please tell me the tools you used for ion torrent RNA-seq data. I'm aware about illumina. Please give me a pipeline of tools which need to be used.

Thank you !!

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written by Vasu Vasu

Thanks for the reply. Are you sure that HISAT pipeline (Stringtie, ballgown) can be used for Ion Torrent data? Do I need to follow any separate command options different from Illumina data?

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written by Vasu Vasu

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