User: Charles Plessy

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

Molecular biologist, open scientist and Debian developer.

Posts by Charles Plessy

<prev • 281 results • page 1 of 29 • next >
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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 3 months ago by Charles Plessy2.5k
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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 3 months ago by Charles Plessy2.5k
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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 4 months ago by Charles Plessy2.5k
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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 5 months ago by Charles Plessy2.5k
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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 5 months ago by Charles Plessy2.5k • updated 5 months ago by d-cameron1.9k
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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 6 months ago by Charles Plessy2.5k
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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 6 months ago by Charles Plessy2.5k
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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 6 months ago by Charles Plessy2.5k
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Comment: C: Login with identity providers: can we have an alternative to Google?
... Cool; I missed it; thank you. Closing this post accordingly. ...
written 6 months ago by Charles Plessy2.5k
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(Closed) Login with identity providers: can we have an alternative to Google?
... It was convenient to use GitHub as an identity provider. Will it have a chance to come back? Alternatively, how about GitLab or ORCID? ...
meta written 6 months ago by Charles Plessy2.5k

Latest awards to Charles Plessy

Scholar 3 months ago, created an answer that has been accepted. For A: Map human cell line RNA-seq data to virus
Scholar 3 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Popular Question 3 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 4 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 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 ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 8 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 11 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
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.
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 16 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Appreciated 16 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 16 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 16 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Commentator 17 months ago, created a comment with at least 3 up-votes. For C: why does this pipe work
Good Answer 18 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Scholar 18 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 18 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes

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