User: Charles Plessy

gravatar for Charles Plessy
Charles Plessy2.7k
Reputation:
2,710
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Location:
Japan
Website:
http://population-tran...
Last seen:
5 months ago
Joined:
6 years, 2 months ago
Email:
c***************@plessy.org

Molecular biologist, open scientist and Debian developer.

Posts by Charles Plessy

<prev • 285 results • page 1 of 29 • next >
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Comment: C: Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
... As I just found this old post, I would like to comment that I am not using this script anymore. Instead I load the GENCODE file in R and parse it with Bioconductor in functions of the [CAGEr](bioconductor.org/packages/CAGEr) package such as [ranges2annot](https://github.com/charles-plessy/CAGEr/blob ...
written 5 months ago by Charles Plessy2.7k
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Comment: C: Is possible to convert BSgenome object to GRange?
... I think it would be great to promote this comment as an answer, so that it can be upvoted at the top. ...
written 5 months ago by Charles Plessy2.7k
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Job: Postdoctoral Position in Population Genomics of an Amazing Animal
... We seek a talented, motivated computational biology postdoc to join Nick Luscombe’s Genomics and Regulatory Systems Unit ([www.luscombelab.org](https://www.luscombelab.org)) at the Okinawa Institute of Science and Technology Graduate University ([OIST](https://www.oist.jp)). The postdoc will apply s ...
genome evolution job population nanopore tunicate written 16 months ago by Charles Plessy2.7k
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Alternative to tblastn in which one can define a custom genetic code
... I am studying the mitochondrial genome of a tunicate, and in these animals there are extraordinary variations in terms of gene contents and genetic code compared to other chordates (their parent clade). I am searching whole-genome assembly multi-fasta files with `tblastn`, but in recent versions it ...
mitochondria alignment genetic code blast written 16 months ago by Charles Plessy2.7k
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Answer: A: Bowtie alignment of piRNAs to find potential targets
... Or maybe you can use [LAST](http://last.cbrc.jp) with a custom [seeding scheme](http://last.cbrc.jp/doc/last-seeds.html) ? ...
written 2.3 years ago by Charles Plessy2.7k
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Answer: A: Bowtie alignment of piRNAs to find potential targets
... How about running the alignment tolerating 3 mismatches anywhere, and then filtering the results using the CIGAR string ? (You would need an aligner that produces CIGAR strings distinguishing matches (`=`) and mismatches (`X`); I do not remember if `bowtie` does). ...
written 2.3 years ago by Charles Plessy2.7k
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Comment: C: Is there an R function that transforms a decimal SAM FLAG into a list of strings
... Tip of the day: to save typing, declare integer type with the `L` suffix as in `1024L`, instead of `as.integer(1024)`. ...
written 2.4 years ago by Charles Plessy2.7k
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Comment: C: changing the name of files
... And to make things even more complicated, the `rename` tool linked by https://www.biostars.org/u/18998/ in another answer is not the same as the `rename` tool in this answer, which is available at , and in the `rename` package on Debian and related systems. ...
written 2.4 years ago by Charles Plessy2.7k
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Best DOI provider for a custom genome index ?
... I am preparing a custom genome index (for sequence alignment), that combines hg38 plus other reference sequences subjected to more frequent updates (HPV and mycoplasma genomes, mostly updated by addition of new ones). I intend to use it in a publication and I would like to keep a precise descriptio ...
genome metadata doi written 2.5 years ago by Charles Plessy2.7k • updated 2.5 years ago by d-cameron2.2k
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Answer: A: Building bioinformatics tools in Ubuntu 17.10
... Ubuntu Bionic already comes with a [bowtie 2.3.4.1 package](https://packages.ubuntu.com/search?suite=bionic&keywords=bowtie2). It was compiled with GCC7 as you can see from the [build logs](https://launchpadlibrarian.net/356214175/buildlog_ubuntu-bionic-amd64.bowtie2_2.3.4.1-1_BUILDING.txt.gz). ...
written 2.6 years ago by Charles Plessy2.7k

Latest awards to Charles Plessy

Popular Question 5 months ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Appreciated 15 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Popular Question 15 months ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Popular Question 15 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 2.3 years ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Scholar 2.3 years ago, created an answer that has been accepted. For A: Map human cell line RNA-seq data to virus
Popular Question 2.3 years ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Popular Question 2.5 years ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 3.0 years ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 3.0 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 3.3 years ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 3.3 years ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 3.3 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Good Answer 3.3 years ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor

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