[galaxy-user] NGS: Indel Analysis tool order

Hello! I have a question about the NGS: Indel Analysis toolset in Galaxy. I have aligned my samples from Illumina's HiSeq2000 to the reference genome using BWA. I've called SNPs using SAMTools and now need to call indels. Under the NGS: Indel Analysis toolset, I see two optio

Re: [galaxy-user] Cuffdiff question about using an unspecified (?) database/build

t; box for analyses where I provide the fasta and gtf file. Thanks, David -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Friday, August 19, 2011 9:20 AM To: David K Crossman Cc: galaxy-user (galaxy-user@lists.bx.psu.edu) Subject: Re: [galaxy-user] Cuffdiff question

[galaxy-user] Cuffdiff question about using an unspecified (?) database/build

Hello! I have an RNA-Seq project which consists of 5 samples from the species tree shrew. When uploading these fastq files into Galaxy, I chose "unspecified (?)" for the database/build since the latest tree shrew version is not in the drop down list. When using TopHat, Cufflin

[galaxy-user] Cufflinks reporting FPKM values of all zeroes (0)

Hello! I have come across a problem where Cufflinks is reporting all FPKM values as zeroes (0). I have a unique RNA-Seq project from a collaborator where they are studying eyesight by using tree shrews. I found that Ensembl (http://useast.ensembl.org/Tupaia_belangeri/Info/Index

Re: [galaxy-user] using files produced by "Barcode Splitter"

Jeremy, The files need to be groomed using the FastQ Groomer so that they will end up in the fastqsanger state. Then your files will show up in the pull-down menus. David From: galaxy-user-boun...@lists.bx.psu.edu [mailto:galaxy-user-boun...@lists.bx.psu.edu] On Behalf Of Je

[galaxy-user] Analyzing RNA-Seq replicates using Cuff(links/Compare/Diff)

Hello! I have 10 human RNA-Seq samples consisting of 3 groups (2 replicates per group). I have already run each of them through TopHat and Cufflinks on the Penn State Galaxy instance. I am now at a head-scratching moment. I want to use CuffCompare next (in the end I will want

[galaxy-user] Galaxy server issues?

Hello! We uploaded 12 samples to Galaxy last night via FTP. This morning, I went to "Get Data" and clicked on all 12 that were under the FTP location, chose the type of file they were and reference genome and then clicked "Excecute." The 12 moved over to the History panel and

Re: [galaxy-user] Mycoplasma pneumoniae M129 and FH reference genome

Jen, Thanks for the useful tips! Yes, the NCBI bioproject link is the correct source for the FH strain. Thanks, David -Original Message- From: Jennifer Jackson [mailto:j...@bx.psu.edu] Sent: Tuesday, May 31, 2011 10:07 AM To: David K Crossman Cc: galaxy-user

[galaxy-user] Mycoplasma pneumoniae M129 and FH reference genome

Hello! I noticed that Mycoplasma pneumonia M129 and FH are not found in the reference genome in Galaxy. Would it be possible to have both of those in there? Thanks, David ___ The Galaxy User list should be used for the dis

Re: [galaxy-user] RNA seq analysis and GTF files

ssign it a name (i.e. gene_name or gene_id) for it to be recognized and if so, how do you assign column names to GTF files? Thanks, David From: Jeremy Goecks [mailto:jeremy.goe...@emory.edu] Sent: Thursday, April 07, 2011 9:40 PM To: David K Crossman Cc: galaxy-user Subject: Re: [galaxy-user

Re: [galaxy-user] RNA seq analysis and GTF files

Hello! I would like to ask a question related to this thread below. I ran into the same issues as below and was unaware of having to swap some columns around in the GTF file. So, after 'swapping the gene name from the complete table (name2 value, column 12) into the GFT file

[galaxy-user] FASTQ to FASTQSanger using Groomer question

t help me better understand the quality score and which to use? Any info/help would be greatly appreciated. Thanks, David David K. Crossman, Ph.D. Systems Biologist/Analyst/Statistician Heflin Center for Genomic Science University of Alabama at Birmingham 720 20th Street South Kaul Room 420 Bir