User: george.ry

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george.ry980
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Posts by george.ry

<prev • 87 results • page 1 of 9 • next >
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Answer: A: Run a Python program in Ubuntu
... This isn't your problem I don't think ... the package isn't handling it's own imports properly. You probably just need to change `from . import get_version` to `from GFFUtils import get_version`. The program isn't doing anything particularly exciting anyway, though, so you could also just do it in ...
written 7 months ago by george.ry980
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Answer: A: Error while downloading data using SRA toolkit
... As per the link in the error message, SRA has moved from HTTP to HTTPS, rendering all previous versions of the SRA toolkit obsolete. You say you downloaded 2.8.1, but you still appear to be running 2.3.5, so I'd check what version is in your `$PATH` and where you installed the latest version. ...
written 7 months ago by george.ry980
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Comment: C: Parse file to remove two characters from the ends of a lot of lines
... Am I right in guessing that you're on a Mac, then? // EDIT // Answering myself, the answer is that you are. OSX doesn't have GNU sed, so you'll need to install it with homebrew (etc). ...
written 8 months ago by george.ry980
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Answer: A: Parse file to remove two characters from the ends of a lot of lines
... New file: `sed '1~4s/\/1$//' myfile.fq > mynewfile.fq` Inplace: `sed -i '1~4s/\/1$//' myfile.fq` ...
written 8 months ago by george.ry980
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Answer: A: How to draw a phylogenetic tree together with a genome locus structure?
... If you're handy with Python, then [ETE Toolkit][1] will do this and more. [1]: http://etetoolkit.org/ ...
written 10 months ago by george.ry980
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Comment: C: Multiple Sequence Alignment tools
... Unless I'm missing some complexity here, you don't need an MSA to achieve this. A local blast library will do this far more simply. ...
written 10 months ago by george.ry980
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Comment: C: Annotation of repeatative elements
... We need more information on what you're trying to do to answer this properly. However, for 2), RepeatMasker significantly outperforms Censor. Unless you have a reason not to use it, RepeatMasker is basically the *de facto* standard. ...
written 11 months ago by george.ry980
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Answer: A: Split SAM file into smaller SAM files by line count
... I actually end up doing this with some regularity, so here's a smooth all-in-one method: samtools view -H yourfile.bam > header then samtools view yourfile.bam | split - yourprefix -l 8000000 --filter='cat header - > $FILE.sam' or samtools view yourfile.bam | split - yourp ...
written 12 months ago by george.ry980
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Comment: C: What is the future of EMBL-EBI (and European bioinformatics in general) in case
... A monumentally stupid day. Nothing else to say. ...
written 14 months ago by george.ry980
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Comment: C: Retrieve a subset of FASTA from large multi-FASTA file
... This should be an (the) answer, as it's really the only way to go about it! If I had to re-format and re-write every file from which I extract random sequences, the storage array would have a fit! From a practical perspective, if you are actually storing data on a shared array with some kind of ba ...
written 14 months ago by george.ry980

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Teacher 8 weeks ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 7 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Scholar 8 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 9 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Commentator 10 months ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Commentator 15 months ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Scholar 18 months ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Pundit 21 months ago, created a comment with more than 10 votes. For C: Do bioinformaticians often break molecular biologists' hearts by being the first
Appreciated 21 months ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
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Appreciated 21 months ago, created a post with more than 5 votes. For A: Help for changing fasta seq ID
Teacher 21 months ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 2.2 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Commentator 2.2 years ago, created a comment with at least 3 up-votes. For C: Minia bug: max rehashes reached: 65536000 (notify a developer)
Teacher 2.3 years ago, created an answer with at least 3 up-votes. For C: Install bam-readcount with no sudo
Scholar 2.4 years ago, created an answer that has been accepted. For A: Script for extracting atomic position of nucleotide base
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Affymetrix Cel File - Probe Intensity Values To Rgb
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Teacher 3.7 years ago, created an answer with at least 3 up-votes. For A: How To Identify Quantile Normalized Expression Data

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