Ion Torrent Fastq Format Type?

Can anyone confirm whether the Ion-Torrent FASTQ file conforms to Sanger (Phred+33), or one of the others?

I attach a link to the NAR paper for interest sake.

ion-torrent fastq

• 10,271 views • link

updated 6.8 years ago by lakhujanivijay

• written 14.3 years ago by Ian

Does that mean that I can use FASTQC for Ion Torrent data ?

• 0 views • link

written 6.8 years ago by lakhujanivijay

Yes. There is no reason not to.

• 0 views • link

written 6.8 years ago by GenoMax

1 answer

Yes Sanger (phred+33)

• 281 views • link

written 14.3 years ago by Nick Loman •

More posts like this

Variant calling: Samtools QUAL from NGS data Vs. Sanger quality score
written 7.9 years ago by omer.k •

So I've sequenced samples with MinION NGS platform, and analysed for SNPs via SAMtools/BCFtools. To corroborate or reject these SNVs I've sequenced the same samples …
Removal of Prevotella Copri sequence from a FASTQ/A file
written 9.8 years ago by tmad109 •

Hi All, We have fastq files from a gut microbiome projects. I used 16S metagenomic kit from Ion torrent and sequenced them on Ion PGM, …
How To Understand The Encoding And Trim Their Adapters
written 12.6 years ago by bmechuangye •

Hi, I am puzzled how to change the encode to Sanger format phred+33 of the data and how to trim the adapter sequence? I have …
Fastx Invalid Quality Score Value
written 12.7 years ago by sckinta

I have multiple RNAseq libraries to parse, so I wrote a pipeline using bash and submitted them in batch. Most of libraries ran well and …
Ffpe False Positive Variant Calls
written 13.0 years ago by richardc.gsc •

Hi All, When I look in the literature about the FFPE causing changes to DNA, it seems to always cite a spike in C>T and …
Representing Genome Wide Regulatory Elements
written 13.1 years ago by ancient_learner

Hi I want to represent the presence of certain important regulatory elements for each chromosome separately. I came across a particular paper (figure 2) and …
Ion Torrent Mapping
written 14.3 years ago by Ian

I am new to Ion Torrent mapping, but have come to the conclusion that <a href='https://github.com/iontorrent/TMAP'>TMAP</a> is the mapper of choice at the moment. Would …
Where Is The Biomart Sparql Endpoint
written 14.6 years ago by Biogeek •

On their paper here - <a href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175789/">http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3175789/</a> - it is announced that Biomart is available as a SPARQL endpoint. Anyone know where this SPARQL endpoint …
Is There An Implementation Of Dnabit Compress Algorithm?
written 14.6 years ago by Martyix •

I'm looking at: <ul> <li><a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046040/?log$=activity'>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046040/?log$=activity</a> and </li> <li><a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046040/bin/97320630005350S1.pdf'>http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3046040/bin/97320630005350S1.pdf</a> </li> </ul> And the sample implementation of the algorithm seems to be broken (I see …
Full Text Retrieval From Pubmedcentral
written 16.0 years ago by Andrew Su

Anyone know how to extract full-text articles from PubMed Central in some structured format? The page on the <a href="http://www.ncbi.nlm.nih.gov/pmc/about/oai.html">PMC OAI Service</a> seems relevant, but …