[galaxy-user] clipping from 5' end

Hi all, Does anyone know if it is possible to trim/clip a sequence from the 5' end? Thank you. Best, Soetkin. Soetkin Versteyhe, PhD PostDoc University of Copenhagen Faculty of Health Sciences The Novo Nordisk Foundation Center for Basic Metabolic Research Integrative Physiology Blegdamsvej

Re: [galaxy-user] clipping from 5' end

Hello Soetkin, A tools search using the keyword trim will bring up the options in Galaxy, the simplest being the FASTX-toolkit Trim function. To enable searching, use the the Options menu in the top left tool menu panel. Thanks for using Galaxy! Jen Galaxy team

Re: [galaxy-user] clipping from 5' end

Hi, with regard to the 5' clipping: On the main (usegalaxy.org) server: it is possible using the NGS: QC and manipulation = Generic FASTQ Manipulation = FASTQ Quality Trimmer by sliding window. If you are interested, we have recently adapted that tool a bit to improve speed (5'+3' clipping

[galaxy-user] RV: Visual and Conputational Analysis of positive sites in chip-chip data

Hi all We are working with chip-chip data of S. cerevisiae (from Affymetrix) and actually we have two problems and we don´t know if it´s possible to perform in Galaxy: 1. We use the tool intersect to get the annotation of positive genomic regions in our file bed. After, we need calculate

[galaxy-user] Changing Bowtie parameters in TopHat

My apologies if this has been covered before but I am using Galaxy Main and wonder if, when running TopHat, you can modify the mapping parameters used by Bowtie? It seems that the full parameter list for TopHat pertains only to the reads that aren't mapped by Bowtie (the reads spanning splice

Re: [galaxy-user] Changing Bowtie parameters in TopHat

Jeremy, My apologies if this has been covered before but I am using Galaxy Main and wonder if, when running TopHat, you can modify the mapping parameters used by Bowtie? Not all Bowtie parameters can be modified when running Tophat. Which parameters are you looking to modify and why? It

Re: [galaxy-user] Changing Bowtie parameters in TopHat

Hi Jeremy, Thanks for your help. I'm mapping reads from one organism to a related but different organism, so some of the parameters I'd like to adjust are to relax mapping stringency -specifically: -n 3 (allow 3 mismatches in seed) -e 250 (allow cummulative phred score of 250 [or some other

Re: [galaxy-user] RV: Visual and Conputational Analysis of positive sites in chip-chip data

I think closest to what you want to do in galaxy can be done in cistrome http://wiki.g2.bx.psu.edu/Community/Cistrome Unless I am missing some galaxy tool in testing, which other galaxy users more closely following galaxy test can comment on best Abhay 2011/11/16 Mónica Pérez Alegre

Re: [galaxy-user] RV: Visual and Conputational Analysis of positive sites in chip-chip data

I dont think Cistrome can provide sufficient visualization options. In CEAS analysis it can provide overall picture of genome binding regions or some relative binding histograms. I beleive what Monica is asking when one has chip enriched regions how to visualize such selected regions- I will

[galaxy-user] Using Galaxy Cloudman for a workshop

Hi all (especially Enis :) ), We are planning to use Amazon (Galaxy CloudMan) to run a workshop for about 50 people. We won't need to transfer any data during the workshop, but need the virtual cluster to be reasonably responsive and cope with: a) the load on the front end b) the workshop

Re: [galaxy-user] Using Galaxy Cloudman for a workshop

Hi Clare, Jeremy (from the team) ran a similar workshop several months ago and used some resource intensive tools (e.g., Tophat). We were concerned about the same scalability issues so we just started 4 separate clusters and divided the users across those. The approach worked well and it turned