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

2012-06-27 Thread Lilach Friedman
Hi Jennifer, Is there a way to directly upload my files from the public Galaxy to my cloud Galaxy instance (in AWS)? Or should I download them first to my computer, and then to upload them? (It takes a lot of time because of the low uploading speed). Thanks, Lilach 2012/6/26 Jennifer Jackson

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

2012-06-27 Thread Lilach Friedman
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 lilac...@gmail.com Hi Jennifer, Is there a way to directly upload my files from the public Galaxy to my cloud Galaxy

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

2012-06-27 Thread Jennifer Jackson
Hello Lilach, The genome build 'hg_g1k_v37' is build b37 in the GATK documentation. Hg19 is also included (as a distinct build). I encourage you to examine these if you are interested in crossing over between genomes or identifying other projects that have data based on the same genome build.

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

2012-06-27 Thread Jennifer Jackson
Hi Lilach, Regarding the cloud instance, you can load data from the public main instance of Galaxy just like any other URL. On the Get Data - Upload Data form on your cloud instance , paste in the URLs of the datasets from main. The URL can be captured by right-clicking on a dataset's disk

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

2012-06-26 Thread Carlos Borroto
Hi Lilach, Sorry for the late response. Jen just confirmed the disadvantages of my approach. I don't know how difficult could be for you to double check the coordinates you have in your interval file are correct for hg_g1k_v37. If you feel confident they will work and want to proceed, you could

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

2012-06-25 Thread Jennifer Jackson
Hello Lilach, Currently, the human reference genome indexed for the GATK-beta tools is 'hg_g1k_v37'. The GATK-beta tools are under active revision by our team, so we expect there to be little to no change to the beta version on the main public instance until this is completed. Attempting to

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

2012-06-24 Thread Lilach Friedman
Hi Carlos, Thank you very much for this explanation. The format of my intervals file is: chr133289059732890664NM_59_cds_1_0_chr13_32890598_f0+chr1332893213 32893462NM_59_cds_2_0_chr13_32893214_f0+chr133289921232899321 NM_59_cds_3_0_chr13_32899213_f0+chr133290023732900287

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

2012-06-21 Thread Lilach Friedman
Hi Jennifer, Thank you for this reply. I made a new BWA file, this time using the hg19(full) genome. However, when I am trying to use DepthOfCoverage, the reference genomr is stucked on the hg_g1k_v37 (this is the only option to select), and I cannot change it to hg19(full). Most probably,

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

2012-06-18 Thread Jennifer Jackson
Hi Lilach, The problem with this analysis probably has to do with a mismatch between the genomes: the intervals obtained from UCSC (hg19) and the BAM from your BWA (hg_g1k_v37) run. UCSC does not contain the genome 'hg_g1k_v37' - the genome available from UCSC is 'hg19'. Even though these

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

2012-06-18 Thread Hiram Clawson
I'm curious what is this genome called 'hg_g1k_v37' and how does it correspond to NCBI GRCh37 which is identical to UCSC hg19 ? --Hiram Jennifer Jackson wrote: UCSC does not contain the genome 'hg_g1k_v37' - the genome available from UCSC is 'hg19'. Even though these are technically the

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

2012-06-18 Thread Church, Deanna (NIH/NLM/NCBI) [E]
If hg_g1K_v37 == 1000 Genomes version of GRCh37 then it is the GRCh37 Primary assembly + a decoy sequence to try to soak up off target reads. The chromosome coordinates are the same but the sequences included in the packages are different. Here is the description from the 1000 Genomes site: