User: Joshua Orvis

gravatar for Joshua Orvis
Joshua Orvis100
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100
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New User
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Last seen:
4 years, 3 months ago
Joined:
5 years, 2 months ago
Email:
j*****@gmail.com

Posts by Joshua Orvis

<prev • 6 results • page 1 of 1 • next >
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Bwa Indexing Not Automatic?
... I installed a new copy of galaxy today and then added the bwa_wrappers tool. After I upload my reference genome and left/right reads I get output like this each time I try to run bwa for illumina: The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_diff = 2 [bwa_aln] 38bp read ...
alignment bwa written 4.3 years ago by Joshua Orvis100 • updated 4.3 years ago by Jennifer Hillman Jackson23k
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Using Local Files Rather Than Uploading?
... For those setups where the server is running on a large, local file system, is there a method to point Galaxy at a set of files without uploading them through the web server? This both duplicates the data and (for some reason) takes a considerable amount of time to upload. Thanks - Joshua ...
galaxy written 4.5 years ago by Joshua Orvis100 • updated 4.5 years ago by Peter Cock1.4k
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Bwa Failing To Index?
... I just installed a new instance of Galaxy and bwa_wrappers from the main toolshed. I then uploaded a reference genome along with two FASTQ files in order to run "Map with BWA for Illumina". When I run it, I get this error: The alignment failed. Error aligning sequence. [bwa_aln] 17bp reads: max_d ...
alignment bwa written 4.6 years ago by Joshua Orvis100 • updated 18 months ago by 5140796850
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Runtime Data?
... Maybe this is in a simple place and I'm missing it, but where can I find simple runtime data for both individual tools and larger workflow executions? I have run several different versions of a saved history using the API and want to now see how the runtimes differ between them. It can be using th ...
written 5.0 years ago by Joshua Orvis100 • updated 5.0 years ago by Jennifer Hillman Jackson23k
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Comment: C: Gatk Not Running
... I'm having some problems with GATK as well, but do have a functional pipeline that uses the following GATK tools in Galaxy: - Realigner Target Creator - Indel Realigner - Unified Genotyper - Variant Filtration The main problem I'm having with them is that it seems I need to run the fasta/fastq gro ...
written 5.1 years ago by Joshua Orvis100
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Create An Index With Samtools Within A Pipeline?
... I want to make a pipeline that grabs a reference genome, indexes it, then aligns reads to it via bwa. The bwa tool has a menu option for using an index "from the history" (see attached image) but I don't see any option within the bwa wrappers to actually create an index on the fly. This is also tr ...
bam samtools alignment bwa written 5.2 years ago by Joshua Orvis100

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