Question: Quality Stat.
gravatar for Robin Mjelle
7.6 years ago by
Robin Mjelle20
Robin Mjelle20 wrote:
Dear User, I am trying to use the tool "Compute quality statistics<http:"" tool_runner?tool_id="cshl_fastx_qu" ality_statistics="">" in galaxy on Ilumina single reads. The file is 2.3 Gb, fastq format. I have performed Quality format converter on the data set and the format is now qualillumina. Despite of this, galaxy don't recognize any dataset in the workflow to use as input into quality statistics. Any idea why my dataset is not accepted as input? Best, Robin
galaxy • 1.0k views
ADD COMMENTlink modified 7.6 years ago by Jennifer Hillman Jackson25k • written 7.6 years ago by Robin Mjelle20
gravatar for Jennifer Hillman Jackson
7.6 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hi Robin, Run the FASTQ Groomer on your datafile first, then use the result as input to the Compute quality statistics tool. (Skip using Quality format converter). Hopefully this helps, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 7.6 years ago by Jennifer Hillman Jackson25k
gravatar for Peter Cock
7.6 years ago by
Peter Cock1.4k
European Union
Peter Cock1.4k wrote:
Looking at the XML wrapper, it expects fastqsanger ONLY. See fastx_toolkit/fastx_quality_statistics.xml It could in theory take fastqillumina or fastqsolexa as well, I thought there was an open bug report on this issue but I can't find it right now. Certainly fastx_clipper.xml was updated to use the -Q 33 switch only for Sanger quality scores, and from a quick check all the other FASTX tools have this fix except fastx_quality_statistics.xml Peter
ADD COMMENTlink written 7.6 years ago by Peter Cock1.4k
Hi, I recently sent out an email asking if anyone knew much about analysis of SNPs etc and how to visualise them. I got some very useful answers and planned to return to the problem when I got a better chance to work on this in some depth. I now have the time but, like an idiot, I've accidentally deleted those email replies! So can I please ask again, does anyone have experience of SNP analysis and, especially, visualisation that can hold my hand whilst I work this out (apologies to the ones who replied last time but can you get in touch again !)? Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091
ADD REPLYlink written 7.6 years ago by David Matthews630
Hi David, For NGS data, the tools under "NGS: Indel Analysis" can build simple BED files of indels from SAM files that can be viewed in Galaxy (Visualization tab - i.e. Trackster). For viral genomes, you will not be able to use UCSC. The Galaxy 101 tutorial includes some basic SNP analysis and visualization tasks that may help you to orient: You may get some more replies, but to pull up old responses on the galaxy-user and galaxy-dev mailing list, the archives are here: To search, use google and enter: site: plus enter whatever keywords would identify your questions (perhaps your name?) Other list members are encouraged to reply to David's inquiry with more help again, Best! Jen Galaxy team -- Jennifer Jackson
ADD REPLYlink written 7.6 years ago by Jennifer Hillman Jackson25k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 165 users visited in the last hour