Tools for Ion Torrent RNA-Seq data analysis

[bvk]

Hello Everyone,

I'm aware about the tools that need to be used for RNA-Seq data analysis of illumina platform.

But I would like to know what tools need to be used for RNA-Seq analysis of Ion Torrent platform?

For alignment I know that BBMap is faster and does better job. May I know which tools need to be used for the other steps and differential analysis.

Thank you

[GenoMax]

Tools for Illumina should be fine to use for Ion Torrent data as well since you still have fastq data. There may be biases/other issues with Ion torrent that you would need to keep in mind (e.g. homo-polymers) but otherwise use any tools you like.

[bvk]

Thanks for the reply. But I see that Tophat and cufflinks pipeline cant be used for Ion torrent data right. Are you sure that I can use these tools?

Can I also use Hisat2, Stringtie and Ballgown?

Some were saying that BBMap is good for alignment for Ion Torrent data.

[GenoMax]

It is not that it can't be used. It is more that you should not be using TopHat pipeline for any new data. TopHat is in maintenance mode and even its developers recommend that you use HISAT2, their latest creation.

You may need to try a newer aligner (e.g. BBMap, STAR, HISAT2) and see what works best for your data.

[bvk]

Thank you !! Our data is generated from Ion Torrent Amplicon based platform. Do you think Hisat can be used for that? And could you please tell what is the main difference between Ion torrent amplicon and Illumina platform data?

[GenoMax]

Are you referring to targeted amplicon sequencing for RNAseq?

[bvk]

Yes it is Ion Torrent Amplicon Sequencing RNA-Seq. I see that TMAP is the best alignment tool for this data. I would like to know how to do the quantification and how to get the gene-level read counts with this data.

And also could you please tell me what is the exact difference between Illumina and Ion Torrent amplicon based platforms from biology point of view.

[bvk]

Ok. Differences between platforms is found here.

Thank you

[snetmcom]

Yes it is Ion Torrent Amplicon Sequencing RNA-Seq. I see that TMAP is the best alignment tool for this data. I would like to know how to do the quantification and how to get the gene-level read counts with this data.

And also could you please tell me what is the exact difference between Illumina and Ion Torrent amplicon based platforms from biology point of view.

The Ampliseq RNA panels just use tmap and the torrent suite coverage analysis tools. I don't think these libraries should be analyzed as RNAseq data as they are specifically targeted for exons.