Re: [galaxy-user] GATK best practices with local installation of Galaxy

Hi, Camille. If you can find some time to upload some of your bam files, could you please test the revised bam merge tool on http://test.g2.bx.psu.edu/ and let me know how you go. This won't be on the main site until the next scheduled update in a few weeks. If you need this locally, the changes

Re: [galaxy-user] GATK best practices with local installation of Galaxy

Hi, Camille, I can see this really needs a 'proper' fix - preferably taking advantage of the automated header merge. Preserving the metadata from each bam automatically is safer and less error-prone but you could use the existing "Replace sam/bam header" tool to do the surgery once you have a corr

Re: [galaxy-user] visualization

IGV should allow you to do this  but not sure about trackbrowser in Galaxy. Vasu --- On Wed, 8/3/11, Jiannong Xu wrote: From: Jiannong Xu Subject: [galaxy-user] visualization To: "galaxy-user@lists.bx.psu.edu" Date: Wednesday, August 3, 2011, 6:03 PM Hi Jen, I mapped illumine reads to draf

[galaxy-user] visualization

Hi Jen, I mapped illumine reads to draft genomic contigs, and try to visualize the mapping. Is there any way I can use my own reference contigs for visualization? Thanks John Xu NMSU ___ The Galaxy User list should be used for the discu

Re: [galaxy-user] (no subject)

Hello Tarek, If you want to reduce the number of identical reads, then please see the tool "FASTA manipulation -> Collapse sequences". Converting formats would be necessary, the tool "Tabular-to-FASTA" can perform this operation. Best, Jen Galaxy team On 8/2/11 3:57 PM, tarek addwebi wrote:

Re: [galaxy-user] GATK best practices with local installation of Galaxy

Hi Ross, thanks for your answer. I found a dirty fix for merging pairs of bam files, had to change a couple of things in my local installation though. - Add group reads to each BAM file separately using Picard's Add or Replace Groups (with ID

Re: [galaxy-user] GATK best practices with local installation of Galaxy

Camille, thanks for reporting this - I think you have found a bug. We definitely need to be able to preserve metadata when we merge bams. Thanks for your suggestion of using mergeSamFiles - yes, I think it might be a good fix for this problem - but it will take a little while and won't reach the Ma

[galaxy-user] GATK best practices in local installation of Galaxy

Hello guys, I'm trying to run a pipeline of the best practices for snp and indel discovery as described by the people at Broad and I'm running into troubles with the GATK tools in a local installation of Galaxy. The main problem I have is that merging bam files with the samtools merge tool doesn't

[galaxy-user] GATK best practices with local installation of Galaxy

Hello guys, I'm trying to run a pipeline of the best practices for snp and indel discovery as described by the people at Broad and I'm running into troubles with the GATK tools in a local installation of Galaxy. The main problem I have is that merging bam files with the samtools merge tool doesn't

Re: [galaxy-user] (no subject)

On Aug 3, 2011, at 12:49 AM, Addwebi, Tarek wrote: > Hi Dear > Is there anybody whom I can share my data with? I have an important question > that I tried to answer, but I could not. Please see the attachment first, > and let us see the first read in the first row. I need to know how many time