[galaxy-user] SNP calling problems

e not properly indexed. Also Freebayes needs an RG tag. Is there a tool in Galaxy I can use to index BAM files, adding the RG tag? I hope someone can help me! Thank you very much! Debora -- Debora Garzetti, PhD Student AG Rakin Max von Pettenkofer-Institute, LMU Pettenkoferstraße 9A 80336 Munich

[galaxy-user] main galaxy server is down?

psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- Debora Garzetti, PhD Student AG Rakin Max von Pettenkofer-Institute, LMU Pettenkoferstraße 9A 80336 Munich E-mail: garze...@mvp.uni-muenchen.de Phone: +49 (0)89 2180 72915

Re: [galaxy-user] SNP calling problems (Jennifer Jackson)

can I do that? Thank you very much! Debora Message: 3 Date: Fri, 27 Sep 2013 14:02:50 -0700 From: Jennifer Jackson To: garzetti Cc: galaxy-u...@bx.psu.edu Subject: Re: [galaxy-user] SNP calling problems Message-ID: <5245f27a.7020...@bx.psu.edu> Content-Type: text/plain; charset="

[galaxy-user] Problems with Picard and GATK tools

Dear all, I have been trying to analyze some recently acquired WGS reads (re-sequencing with MiSeq) but I am having problems with both Picard and GATK tools and I don't know where the problem is. My fastq reads are already in the sanger/illumina 1.9 format, as recognized by the FastQC tool.

[galaxy-user] Workflow does not run

Hello! I have a question about a workflow I have created from my history. I can edit and view it, but when I try to run it, a white page appears and I cannot do anything. I have created other worflows which perfectly run, but I don't know why this one doesn't. It includes 4 steps for GATK pre-

[galaxy-user] Read simulator

Dear all, I would like to perforn my SNP calling pipeline (for MySeq Illumina reads) to previously sequenced and assembled genomes. Is there any read simulator in the Main Galaxy? I am looking for something like the wgsim algorithm in SAMtools... Thanks! Debora

[galaxy-user] Variant annotation in galaxy

Hallo Galaxy users, I would like to annotate variants (in vcf file) found in my bacterial genomes and look which of them cause non-synonymous mutations. I have found two tools in the Main Galaxy that I can use for this purpose (snpEff and Annovar), but I have problems with them. How can I ch

Re: [galaxy-user] Variant annotation in galaxy

Hi Jen, thanks for your answer! Unfortunatelly I cannot run Galaxy locally (in my Institute we only have Windows computers), but I can try on a cloud. I have a DIAG account, do you know if Galaxy works there? Debora ___ The Galaxy User

[galaxy-user] Concatenate variants from vcf files

Hello, is there a tool in the main Galaxy to extract a fasta alignment of my detected variants from a vcf file? I have 19 samples (plus the reference). Thanks! Debora ___ The Galaxy User list should be used for the discussion of Galaxy an