User: RACHAMPION

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RACHAMPION10
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Last seen:
9 months ago
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1 year, 5 months ago
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R*********@DONS.USFCA.EDU

Posts by RACHAMPION

<prev • 6 results • page 1 of 1 • next >
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Reference genome can it be partial?
... I'm doing an RNA-seq on wheat to get differential expression of wild type vs a mutant. I'm only looking at a few specific genes. The wheat genome has not been fully sequenced, and for this problem it does not need to be. NCBI lists transcriptomes only. Can I use a program (e.g. Tuxedo suite) that re ...
rna-seq alignment tophat assembly written 9 months ago by RACHAMPION10 • updated 9 months ago by shengweima0
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Answer: A: Remove e. coli and vector contaminants from Ilumina reads
... I'll go with Plan 2 because I'm using de Novo assembly. Thus the contigs that I get are a mixture (by BLAST) of T. aestevium, various strains of e. coli, and a variety of vectors. Leaving contaminants in would confuse down stream analysis. A friend uses Plan 2. Yours is additionally helpful in that ...
written 9 months ago by RACHAMPION10
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Remove e. coli and vector contaminants from Ilumina reads
... I ran Trinity (wheat 300 bp paired ends) using Ilumina reads. When I ran BLAST on the contigs, some looked like wheat, and some looked like e. coli, and some looked like vectors (viruses). Is there a way of cleaning the reads before running Trinity to remove the contaminants? I was not able to find ...
assembly written 9 months ago by RACHAMPION10
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Another step to make Trinity output usable with Blast
... I have an output from Trinity that looks like an assembled genome. When I use Blast to check for similarity, I get the message: Your BLAST job specified more than one input sequence. This box lets you choose which input sequence to show BLAST results for. Is there something that I need to do to jo ...
galaxy blast web-blast trinity written 14 months ago by RACHAMPION10 • updated 14 months ago by Jennifer Hillman Jackson23k
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Signing off Galaxy resources
... I am using Galaxy Main (usegalaxy.org), and I will soon be using gigagalaxy. Both applications involve assembly (Trinity and SOAP de novo 2). When I finish, do I have to sign off the computers that run the assembly algorithms, or does this happen automatically? Thanks Rick Champion ...
servers galaxy jobs account assembly written 14 months ago by RACHAMPION10 • updated 14 months ago by Jennifer Hillman Jackson23k
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NCBI genome to Galaxy
... I am trying to download Brachypodium distachyon strain Bd21 chromosome 2, Brachypodium_distachyon_v2.0, whole genome shotgun sequence from NCBI http://www.ncbi.nlm.nih.gov/nuccore/NC_016132.2. NCBI gives me a result in compressed format (.gz) Do I need to uncompress this to get it in to Galaxy? ...
data transfer from ncbi rna-seq written 17 months ago by RACHAMPION10 • updated 17 months ago by Jennifer Hillman Jackson23k

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