User: Charles Plessy

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Charles Plessy2.7k
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Japan
Website:
http://population-tran...
Last seen:
5 months, 1 week ago
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5 years, 3 months ago
Email:
c***************@plessy.org

Molecular biologist, open scientist and Debian developer.

Posts by Charles Plessy

<prev • 283 results • page 1 of 29 • next >
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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 5 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 5 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 17 months 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 17 months 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 18 months 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 19 months 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 19 months ago by Charles Plessy2.7k • updated 19 months ago by d-cameron2.1k
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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 20 months ago by Charles Plessy2.7k
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Comment: C: How to merge quality trimmed interlaced reads?
... Have you looked at the software listed in the post "[Tools to merge overlapping paired-end reads](https://www.biostars.org/p/225683/)"? ...
written 20 months ago by Charles Plessy2.7k
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Comment: C: Login with identity providers: can we have an alternative to Google?
... Hello Charles Plessy! We believe that this post does not fit the main topic of this site. No need since there is biostar.slack.com. For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell ...
written 20 months ago by Charles Plessy2.7k

Latest awards to Charles Plessy

Teacher 14 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 14 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Popular Question 14 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 14 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 17 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Scholar 17 months ago, created an answer that has been accepted. For A: Map human cell line RNA-seq data to virus
Popular Question 17 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 18 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 19 months ago, created a question with more than 1,000 views. For Parsing GENCODE GTF to simpler BED files: am I reinventing the wheel ?
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 22 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 2.0 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
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
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Good Answer 2.5 years ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Appreciated 2.5 years ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 2.5 years ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Commentator 2.6 years ago, created a comment with at least 3 up-votes. For C: why does this pipe work

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