DiscoSNP++ results analysis

Question

[gadicherla.ramya]

Hi all,

I have just started using the DiscoSNP++ tool. I have been facing some problems after I generate the data.I have sequence of a bacteria which was obtained by denovo assembly on Ion torrent platform. I have to use this data as a reference for calling SNP's across 6 samples. I have come across DiscoSNP++ tool which seems good. My questions are:

1. Can I use this tool for calling SNP's from data generated from Iontorrent platform?
2. Should I call SNP's from one sample and then compare it with others or all the sample's data can be combined and called for SNP's?
3. I get a format when I use a single sample file and a different profile if I using more datasets of different samples?
4. How do I infer the generated data? I mean the interpretation.

Thanks in advance

Ramya

Answer 1

[pierre.peterlongo]

Hi Ramya,

Sorry for this very late answer. I guess it's too late, but anyway, maybe theses answers may help:

1. Can I use this tool for calling SNP's from data generated from Iontorrent platform?

We have no feed back on applying discoSnp on this kind of data. Thus if you've any feedback, it would be warmly welcome

2. Should I call SNP's from one sample and then compare it with others or all the sample's data can be combined and called for SNP's?

The discoSnp spirit is to call SNPs from all read sets together, without using the reference while making this call. Your assembly could thus be used mainly for locating the predictions.

3. I get a format when I use a single sample file and a different profile if I using more datasets of different samples?

No, the main results files (fasta and vcf) contain the read coverage per input read set.

4. How do I infer the generated data? I mean the interpretation.

Results are provided both in a fasta format and in a VCF format. These two formats can be used in classical downstream analysis.

Pierre