can I use ion torrent fastq in illumina pipeline?
Hi,
We have some sequence data from Ion Torrent. I have both the BAM files and fastq. Our collaborators have an analysis pipeline set up for Illumina data (what they usually use). I was told that there were differences between the two and extra steps would be needed to make the ion torrent compatible with an illumine analysis pipeline. However, I can't find any information about this anywhere. Is this true? What steps are these?
Thank you!
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Fastq format is a standard for all sequencing technologies. Actual encoding may differ but you should be able to use Ion torrent files in your pipeline. That said there may be a bias/batch effect between the sequencing technologies. So be cautious about comparing results across them.
I think these differences may rely on the quality control step. For instance, Ion Torrent uses single-nucleotide addition, which can increase the number of homo-polymers, so you may need to check for those, whereas Illumina relies on cyclic reversible termination, where homo-polymers are few or negligible and substitutions are more common.
Other thing that I'm not sure because I never worked with Ion Torrent, but I don't think that this technology is able to produce paired-end data as Illumina does (be careful - I'm not sure). If so, you might have other step that you may need to adapt (although you can also have only single-end data with Illumina - so it depends which parameters are you applying).