Re: [galaxy-user] Problem with Depth of Coverage on BAM files (GATK tools)

May I join to the question of Carlos? what is exactly hg_g1k_v37? and how can I get the intervals of specific genes in this format? Thanks, Lilach 2012/6/27 Lilach Friedman > Hi Jennifer, > Is there a way to directly upload my files from the public Galaxy to my > cloud Galaxy ins

Re: [galaxy-user] Problem with Depth of Coverage on BAM files (GATK tools)

links on the GATK tools can provide more information about > sources, including links on the GATK web site which will note the exact > contents of the both of these genome versions, downloads, and other > resources. > > Hopefully this helps to clear up any confusion, > > Best, > &

Re: [galaxy-user] Problem with Depth of Coverage on BAM files (GATK tools)

NM_59_cds_4_0_chr13_32900238_f0+etc... Can you please explain me how to change this format so I will be able to give it as an input to DepthOfCoverage Thanks, Lilach 2012/6/21 Carlos Borroto > On Thu, Jun 21, 2012 at 10:50 AM, Lilach Friedman > wrote: > > Hi Jennifer, > > Thank

Re: [galaxy-user] Problem with Depth of Coverage on BAM files (GATK tools)

l > need to be careful with genome database assignments, etc. Following the > links on the tool forms to the GATK help pages can provide some more detail > about expected inputs, if this is something that you are going to try. > > Good luck with the re-run! > > Jen > Galaxy t

Re: [galaxy-user] generate pileup not working?

en > Galaxy team > > > > > On 6/14/12 1:36 PM, Lilach Friedman wrote: > > Hi, > I am trying to do variants call with "generate pileup". > My steps where: > 1. BWA > 2. select only lines with the pattern Matching pattern: XT:A:U > 3. SAM-to-BAM > &

[galaxy-user] Problem with Depth of Coverage on BAM files (GATK tools)

Hi, I am trying to used Depth of Coverage to see the coverages is specific intervals. The intervals were taken from UCSC (exons of 2 genes), loaded to Galaxy and the file type was changed to intervals. I gave to Depth of Coverage two BAM files (resulted from BWA, selection of only raws with the Ma

[galaxy-user] generate pileup not working?

Hi, I am trying to do variants call with "generate pileup". My steps where: 1. BWA 2. select only lines with the pattern Matching pattern: XT:A:U 3. SAM-to-BAM 4. then I tried to use "Generate pileupfrom BAM dataset" However, it does not w

Re: [galaxy-user] Galaxy in AWS AMI

http:///), what do you see? > > -Dannon > > > On Jun 13, 2012, at 5:47 PM, Lilach Friedman wrote: > > > Hi, > > Can somebody please help me? > > I'm trying for hours to connect to Galaxy on Amazon EC2. I did > everything according the instructions, b

Re: [galaxy-user] Galaxy in AWS AMI

and I terminated a created from the beginning new instanced for the last several hours (at least 5 different instances). All don't work. Lilach 2012/6/14 Lilach Friedman > Hi, > Can somebody please help me? > I'm trying for hours to connect to Galaxy on Amazon EC

Re: [galaxy-user] input for GATK DepthOfCoverage

I fixed it, Thanks. It was because I aligned to different genomes in BWA and GATK steps 2012/4/3 Lilach Friedman > Hi Galaxy Team, > I'm trying to use GATK DepthOfCoverage, and to give a BAM file of alined > results as input. > > > My steps were: > 1. BWA alignment

[galaxy-user] input for GATK DepthOfCoverage

Hi Galaxy Team, I'm trying to use GATK DepthOfCoverage, and to give a BAM file of alined results as input. My steps were: 1. BWA alignment 2. SAM-to-BAM 3. rmdup. when I'm trying to give 3 (rmdup results) as an input to GATK DepthOfCoverage, an error appears: " Sequences are not currently avai

Re: [galaxy-user] USing GATK DepthOfCoverage with all exon enriched data

ilach 2012/4/2 Lilach Friedman > Hi, > > I have NGS results of DNA enriched for exons with an AllExon kit (Agilent). > I have a bed file with the list of targeted sequences. > I want to use GATK DepthOfCoverage to compare the results to the bed file > and to get all the targets

[galaxy-user] USing GATK DepthOfCoverage with all exon enriched data

Hi, I have NGS results of DNA enriched for exons with an AllExon kit (Agilent). I have a bed file with the list of targeted sequences. I want to use GATK DepthOfCoverage to compare the results to the bed file and to get all the targets that were covered by _