SNP single end read

Question

[Gabh]

Hello everyone

I am new working with sequencing data, my laboratory has an Ion Torrent PGM sequencer. I have read that the sequences are single end reads, is it possible that with this data I can identify SNP if I do not have a reference genome? Thanks

Answer 1

[Titus]

Hi , To detect SNP you need to have a reference to compare your sample to something ! Are you in a specific organism ? By the way if you have a whole sequencing organism and multiple samples you can create your own reference and then align and call your variant in your different sample. By the way are you sure you speak about SNP and not variants ?

Best

Answer 2

[Raony Guimarães]

Yes it's possible.

Take a look at:

DiscoSnp is designed for discovering all kinds of SNPs (not only isolated ones), as well as insertions and deletions, from raw set(s) of reads. https://github.com/GATB/DiscoSnp

Reference-free SNP detection: dealing with the data deluge https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4333369/

SNP calling from RNA-seq data without a reference genome: identification, quantification, differential analysis and impact on the protein sequence https://academic.oup.com/nar/article/44/19/e148/2468394 and http://kissplice.prabi.fr/documentation/