User: glarue

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glarue0
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Posts by glarue

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very high maximum-likelihood dS values from PAML
... I have a set of putative paralogous transcript pairs (identified via reciprocal BLASTing) that I've aligned at the protein level and backtranslated. I would like to calculate dS for each pair. I have run the alignments through PAML (nucleotide), but am getting very high (>60) dS values for many ...
dn/ds alignment paml written 14 days ago by glarue0 • updated 14 days ago by Hussain Ather510
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Comment: C: what is the problem with using clustal to do pairwise alignment?
... Thanks for the response. What I'm after, though, is a better understanding of *why* EMBOSS recommends against using Clustal for pairwise alignments - presumably they're worse than those produced by, say, NEEDLE, but in what way? What sort of issues might I see in the alignments that would be amelior ...
written 14 days ago by glarue0
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Comment: C: what is the problem with using clustal to do pairwise alignment?
... Good point - no, they were both set to use the default values. I can't figure out how to set the gap penalties for Clustal Omega, but using ClustalW I tried setting the values to be the same as NEEDLE and this resulted in yet another, different, alignment. ...
written 22 days ago by glarue0
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Comment: C: what is the problem with using clustal to do pairwise alignment?
... So, I ran a comparison between Clustal Omega and NEEDLE (EMBOSS's recommended pairwise alignment tool) and, disconcertingly, with default options they both definitely give different alignments: ![different alignments][1] By eye, I guess the Clustal ones do seem worse but I'm not confident in my abi ...
written 22 days ago by glarue0
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what is the problem with using clustal to do pairwise alignment?
... I have a set of putatively-paralogous protein sequence pairs that I'm trying to align. I (naively) used Clustal Omega to generate pairwise alignments, but am getting some weird downstream results (abnormally high dS values between many pairs) so I went back through the documentation and noticed that ...
alignment written 23 days ago by glarue0 • updated 23 days ago by Hussain Ather510
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Answer: A: Getting genbank annotation file from JGI
... AFAIK, JGI does not provide data in GenBank format, so you will have to use a tool to convert the FASTA + GFF3 combo to GenBank. Here is a discussion of one such tool from EMBOSS. If you're going to be pulling multiple datasets from JGI and you'd like to use the command line, you may find useful a ...
written 2.2 years ago by glarue0
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Answer: A: How To Retrieve Data From Jgi Automatically Given A Set Of Ids?
... I know this is a late response, and it may not do exactly what you need, but feel free to check out a script I wrote to do something similar here: https://github.com/glarue/jgi-query   It's written in Python and runs from the command line. I haven't tested it on Mac or Windows, but it should (theo ...
written 2.4 years ago by glarue0
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Comment: C: fastq-dump stream to named pipe (fifo) to Trinity
... Thanks for this. It got me on (what I think will be) the right track. ...
written 3.0 years ago by glarue0
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Comment: C: fastq-dump stream to named pipe (fifo) to Trinity
... Thanks for the response! I am unsure of the advantage of --split-spot over --split-files, but you've outlined the general strategy I've decided on. I've messed around a bit with some simple awk regex parsing of the convolved --split-files -I -Z output, where the -I flag should allow me to separate t ...
written 3.0 years ago by glarue0
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fastq-dump stream to named pipe (fifo) to Trinity
... So, fastq-dump has the ability to be run on just an SRA file accession number, such that the SRA is converted to FASTQ on-the-fly, and the SRA doesn't have to be written to disk. I'm curious whether it would be possible to use fastq-dump to write to a named pipe (using mkfifo) and feed that into an ...
next-gen fastq-dump rna-seq sequencing written 3.0 years ago by glarue0 • updated 2.3 years ago by Biostar ♦♦ 20

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Popular Question 2.1 years ago, created a question with more than 1,000 views. For fastq-dump stream to named pipe (fifo) to Trinity

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