[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

[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,

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

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 about using an unspecified (?) database/build

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

[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

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

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] RNA