Yvan Le Bras reminded us today that everyone can analyse RADseq data in Galaxy.
RADSeq combines two simple molecular biology techniques with Illumina sequencing: the use of restriction enzymes to cut DNA into fragments (as for RFLPs and AFLPs), and the use of molecular identifiers (MID) to associate sequence reads to particular individuals. This delivers high-resolution population genomic data — thousands of sequenced markers across many individuals — for any organism at reasonable costs.
Yvan and his team also created some training materials which you can find in the Galaxy Training Network (GTN).
Following #RADseq question on #usegalaxy help forum, I am retrying our training material on last Stacks version on https://t.co/Ydhnaq1889 #PNDB to create a @GEOBON_org #EBV workflow for intraspecific genetic diversity on the cloud & from my smartphone (baby is sleeping ;) ) pic.twitter.com/kShMZhphWx— Yvan Le Bras (@Yvan2935) March 13, 2021
And using Rule based upload really simplify the process of renaming datasets in the same time we download data from url for this training "RAD-Seq to construct genetic maps" https://t.co/NCuoQ5GZ2D ! Amazing #usegalaxy functionality! I have to update the tuto! pic.twitter.com/pgCuBwqXSA— Yvan Le Bras (@Yvan2935) March 13, 2021
Have to build a "population map"? No problemo ;) using "text manipulation" tools, I created one directly writing names of datasets on new ones, some "select 1st" "cut columns" "concatenate" & "create column", & capturing this process to a workflow so I can free disk space pic.twitter.com/GzmMQWGD4X— Yvan Le Bras (@Yvan2935) March 13, 2021
And you know what? You can help adding scientific information to existing #citizenscience data from @VigieNature Spipoll waiting the end of your @GEOBON_org Genetics #EBV workflow execution ;) #GAPARS #PNDB #MOODA #crowdsourcing pic.twitter.com/ru4VjVOUox— Yvan Le Bras (@Yvan2935) March 13, 2021
After morning #RADseq based Genetic map, now population genomics study in #usegalaxy again with Stacks to generate @GEOBON_org #EBV Genetic differentiation. Data import, quality check of filtered vs unfiltered RAD from 16 samples... In my smartphone screen with my ~🌭 fingers ;) pic.twitter.com/e4yhZCmT8P— Yvan Le Bras (@Yvan2935) March 13, 2021
Generating a population map "on the fly" copied/pasted on the #usegalaxy data upload interfaces. Then, let's go to build loci and.. did I mention that having the display of the training material inside Galaxy-E #PNDB is ... Amazzing !!! So efficient (notably on phone with 🌭;) )! pic.twitter.com/iBRzpuhGDV— Yvan Le Bras (@Yvan2935) March 13, 2021