User: Kelly Vincent

gravatar for Kelly Vincent
Kelly Vincent340
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340
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New User
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Last seen:
6 years, 11 months ago
Joined:
8 years, 3 months ago
Email:
k********@bx.psu.edu

Posts by Kelly Vincent

<prev • 34 results • page 1 of 4 • next >
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Answer: A: Generate Pileup -V
... Matthew, Galaxy's pileup samtools wrapper does not use -v at all. Setting the 'Whether or not to print only output pileup lines containing indels' option to 'Print only lines containing indels' sets -i. Thanks, Kelly ...
written 7.0 years ago by Kelly Vincent340
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Answer: A: Adding A Reference Genome
... Jeremy, You can definitely ask for new genomes. We frequently add them. This particular genome is already on my working list--we've run into a bit of a snag involving permissions and are trying to figure it out. So I can't promise it will be added or say when if it will be. If you do want to upload ...
written 7.0 years ago by Kelly Vincent340
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Comment: C: Error Occurred When Converting The Solid Output To Fastq
... Mike, There actually is not a way to get the deleted base(s) from the SAM alone, since SAM displays only the read and not the reference. Thanks, Kelly ...
written 7.0 years ago by Kelly Vincent340
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Answer: A: Sam To Bam Conversion Problem
... Hemant, This is really odd, and definitely not what should be happening. Would you mind sharing your history with me so I can take a closer look? While I'm looking into it, you should be able to manually change the database to ce6 and then run SAM-to-BAM. We have everything needed for ce6. Thanks ...
written 7.2 years ago by Kelly Vincent340
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Comment: C: Add Other Genomes To Galaxy
... Hi, Hydra_JCVI is now available in Galaxy for several tools, including NGS analysis. Let us know if you run into any problems using it. Regards, Kelly ...
written 7.2 years ago by Kelly Vincent340
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Answer: A: Nr Data For Instantiation
... Hi, You can direct them to https://bitbucket.org/galaxy/galaxy- central/wiki/NGSLocalSetup . You (or they) should also consider signing up for our galaxy-dev mailing list, which is for helping with local installations rather than our public site (http://lists.bx.psu.edu/listinfo/galaxy-dev). Let us ...
written 7.2 years ago by Kelly Vincent340
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Answer: A: Upload Of Zea Mays Genome To Galaxy?
... Karl, Zea mays is now available as a general database/build label. The full value is "Zea_mays_B73_RefGen_v2", but searching for any part of that or "maize" will bring it up. Thanks for using Galaxy. Regards, Kelly ...
written 7.2 years ago by Kelly Vincent340
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Answer: A: Indel Output - What Is This Mystery Column?
... John, It is the number of reads that had this exact insertion, as you guessed. Let us know if you have further questions. Regards, Kelly ...
written 7.3 years ago by Kelly Vincent340
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Answer: A: Upload Of Zea Mays Genome To Galaxy?
... Karl, Zea mays is available for use under the NGS tools. I did notice that it is not available as one of Galaxy's genome/database labels (such as on upload), but this is an oversight that will be corrected ASAP. You can still use the mapping tools in the meantime. Regards, Kelly ...
written 7.3 years ago by Kelly Vincent340
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Answer: A: Help W Sam To Bam
... Hi Dan, The problem is that your FASTA file has a blank lines in it (the first is line 448). You can get rid of them within Galaxy with the Select tool (under Filter and Sort). Select the NOT Matching option and enter "^$" (without the quotes) into the pattern box. This will remove all lines that h ...
written 7.5 years ago by Kelly Vincent340

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