I want to run SHRiMP on SOLiD data, but despite reading the manual I can't find a parameter that allows me to give the .qual file as input. Does SHRiMP not consider quality values at all?
-
-
Probably not. Shrimp is a tool from the corona-lite days. Back then the qual values were pretty much ignored by most tools. I think it was not until BioScope that qual values started being used in ABI's pipeline.Originally posted by agc View Post
--
Phillip -
A new version of SHRiMP was released just last month, so it can't be that outdated. And I think I saw somewhere that it does take quality values into consideration.Comment
-
Yes, perhaps http://compbio.cs.toronto.edu/shrimp/HISTORY:Originally posted by agc View Post
2.0.2: Sep 20, 2010
[...]
- Added --bfast option that performs global color space alignments
along with reporting color space base qualities
But this does not indicate that quality values are used in mapping, only that with the --bfast option that "color space base qualities" are reported.
--
PhillipComment
-
SHRiMP for now only reports the qualities (per-color, and also per-base in the exact same way as bfast). They are not (yet) used for actual mapping, though that is very high on our agenda.
-MikeComment
-
It's still the case, isn't it? The qualities for individual bases are not used in actual alignment?Comment
-
SHRiMP has been using mapping quality values since v2.2.0 in August 2011. If the reads are given in .fasta files, all colors use a default qv corresponding to 3% error rate (about 17). If they are given in fastq files, the qualities are interpreted according to the PHRED value and used as integral part of the alignment. It doesn't take .qual input directly. See such options as --pr-xover, --min-avg-qv, --qv-offset, --ignore-qvs in README.-- Matei DavidComment
-
Tumors contain complex mixtures of cell populations that evolve in response to treatment and host-specific factors. Tissue biopsies provide only static snapshots of a tumor’s state. But what if we could follow that evolution over time using a minimally invasive technique?
Liquid biopsies can detect tumor-derived material circulating in the bloodstream, providing a way to study treatment response, detect emerging resistance, and discover new biomarkers. Circulating...Yesterday, 09:55 AM -
Researchers using sequencing and genomics tools often have to make trade-offs. They can choose between speed or scale, short reads or long-range information, or targeted panels or a view of the whole transcriptome. New technologies that have been released this year are built to address those tough choices.
We asked six companies the same four questions to learn about their latest products. The new technologies bring a lot to the table, including rethinking sequencing...
Comment