User: Richard Smith-Unna

Reputation:
130
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UK
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http://www.blahah.net/
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blahah404
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Google Scholar Page
Last seen:
3 years, 11 months ago
Joined:
7 years, 4 months ago
Email:
r**************@gmail.com

Plant biologist, data analyst, bioinformatician and programmer at the Millennium Seed Bank.

Posts by Richard Smith-Unna

<prev • 13 results • page 1 of 2 • next >
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Answer: A: Is there any tool or script to evaluate transcriptome assembly quality in terms
... Transrate (http://hibberdlab.com/transrate/) does these things. You give it your assembly (or multiple assemblies) and the reads used to generate them, and it outputs a lot of summary statistics about the assembly. These include the accuracy and completeness of the assembly. It also evaluates each ...
written 4.2 years ago by Richard Smith-Unna130
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Answer: A: merged transcripts from RNA de novo assembly to create a reference transcriptome
... corset [software | paper] is much better at merging transcriptome assemblies than cd-hit-est. Specifically it is a tool for clustering contigs in a transcriptome assembly, but this makes it useful for merging, as demonstrated in the paper. ...
written 4.6 years ago by Richard Smith-Unna130
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Comment: C: Sequenceserver: Easily Deploy A Custom, User-Friendly Blast Webserver
... We're also using SequenceServer on the C4 rice project and with data from 1KP to offer BLASTing against out de-novo transcriptome assemblies. It's extremely easy to install. Plus it's in Ruby, so easy to modify :). I'm planning to throw in some code to allow overlaying annotation and expression data ...
written 5.6 years ago by Richard Smith-Unna130
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Answer: A: How To Do Pathway Analysis With Rna Data Which Are Not Pure
... First, you should decontaminate your reads. If you know that you've got bacterial contamination, and you know which bacteria are contaminating, you can filter out those reads by mapping them against the bacterial genomes using bowtie2 with the `--un-conc` setting to output the reads which don't alig ...
written 5.8 years ago by Richard Smith-Unna130 • updated 4 months ago by RamRS21k
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Answer: A: How Can I Obtain Genome Scaffolds Using Paired End 454 Reads And An Hybrid Assem
... I would try using [SSPACE][1] and [GapFiller][2] in that order. An alternative is to use SGA - [see the wiki for instructions][3]. [1]: http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/ [2]: http://www.baseclear.com/landingpages/basetools-a-wide- ...
written 5.8 years ago by Richard Smith-Unna130 • updated 4 months ago by RamRS21k
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Answer: A: Minimum Or Optimal Rpkm Value To Find If A Transcript Is Significant
... It really depends what you mean by significant? Reading between the lines, it seems as though you want to try to separate 'real' contigs from assembly artefacts. If that's the case, you should think carefully before discarding transcripts with a low RPKM. There is no minimum - a contig representing ...
written 5.8 years ago by Richard Smith-Unna130
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Answer: A: Find Mirna Sequences
... Your method sounds fine, although I would do this using [Ensembl BioMart][1], simply because the feature is already built in, as follows: 1. Choose homo sapiens dataset 2. Set your list of gene IDs as the filter 3. Choose sequences: upstream flank and downstream flank as attributes. You can do ...
written 5.8 years ago by Richard Smith-Unna130 • updated 4 months ago by RamRS21k
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Comment: C: Should I Start With Python 3?
... I would say something like ruby is better for learning OOP, and more useful for scientists. That being said, one can easily learn excellent dev practices in python to start with. MIT teaches their CS majors in python, for good reason. ...
written 6.4 years ago by Richard Smith-Unna130
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Comment: C: Where/How To Assess Which Bioinformatics Tools/Databases Are Most Used/Accessed?
... Most academic and other large institutions have a small external IP range - going by unique IP only will probably exclude more true downloads than duplicates (though I can't immediately think of a way of quantifying whether that's true). ...
written 6.4 years ago by Richard Smith-Unna130
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Comment: C: Blast Result Matching Both Of Two Query Sequences?
... Thanks - this also worked. Great tip! ...
written 7.3 years ago by Richard Smith-Unna130

Latest awards to Richard Smith-Unna

Teacher 4.1 years ago, created an answer with at least 3 up-votes. For A: merged transcripts from RNA de novo assembly to create a reference transcriptome
Teacher 4.6 years ago, created an answer with at least 3 up-votes. For A: merged transcripts from RNA de novo assembly to create a reference transcriptome
Supporter 5.2 years ago, voted at least 25 times.
Autobiographer 5.2 years ago, has more than 80 characters in the information field of the user's profile.

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