User: Charles Plessy

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Charles Plessy2.3k
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Japan
Website:
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17 hours ago
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Posts by Charles Plessy

<prev • 249 results • page 2 of 25 • next >
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Must there be spaces after "ORIGIN" in GenBank records ?
... I found that the virus genomes distributed in GenBank format by the [PaVE](https://pave.niaid.nih.gov/) site are not parsed correctly by the [`genbankr`](https://bioconductor.org/packages/genbankr) Bioconductor package, because there are no spaces after the "ORIGIN" field. Either the package is too ...
genbank written 29 days ago by Charles Plessy2.3k
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Comment: C: Stranger Things: unexpected limitations of popular tools
... I do not see how it can be made useful. For instance, in the example below, let's imagine an index containing the sequence of chromosomes *a*, *b*, *c* and *d* (in that order), and two pairs (`-> / <-` and `=> / <=`), then only the pair `-> / <-` can be marked *proper*, most of the ...
written 5 weeks ago by Charles Plessy2.3k
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Answer: A: Stranger Things: unexpected limitations of popular tools
... The index in BWA stores the reference sequences in a contiguous manner, therefore when the first read of a pair aligns very near the end of a chromosome and the second read aligns very near the beginning of the next chromosome, the pair may be marked as *proper*. Now I always postprocess `bwa aln` w ...
written 5 weeks ago by Charles Plessy2.3k
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Comment: C: samtools installation errors
... If you have administrator privileges (and therefore can use `sudo`) you can also try to install samtools from your package manager. For instance on Debian and Ubuntu: `sudo apt install samtools`. It may not be the latest version, though backports often get eventually provided. ...
written 5 weeks ago by Charles Plessy2.3k
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Answer: A: rRNA detection (for contamination) in RNA-seq
... You can count or filter out rRNA reads from FASTQ files (single- or paired-end) using [TagDust](http://tagdust.sourceforge.net) (and do many other things). ...
written 6 weeks ago by Charles Plessy2.3k
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Comment: C: Removing PCR duplicates from .fastq without .bam alignment
... Just for the record: FastUniq can not account for sequencing errors (which can be a strong limitation). Here is a quote from the authors' article ([Xu _et al._, 2012](http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0052249)). > There were some differences in levels of duplicates ...
written 8 weeks ago by Charles Plessy2.3k
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Comment: C: Transform a GTF file into a data frame in R
... Can you transform your comment into a formal answer, by clicking on "moderate" and selecting the appropriate option, so that cristian can "accept" the answer ? This will make the information clearer for the future readers ! ...
written 9 weeks ago by Charles Plessy2.3k
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Comment: C: Renaming All Files In A Directory With A Perl Script
... By the way, on Debian system (and probably Unbuntu too), Perl's `rename` command is being moved to the `rename` package. In future releases (Buster, ...) [the `perl` package will not provide the `rename` command anymore](https://bugs.debian.org/735134). ...
written 10 weeks ago by Charles Plessy2.3k
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Comment: C: Genome Browser suggestions
... It's work in progress. At the moment you would need to contact the browser admin. ...
written 11 weeks ago by Charles Plessy2.3k
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Answer: A: Genome Browser suggestions
... How about [ZENBU](http://fantom.gsc.riken.jp/zenbu) ? Here is an example illustration that I made starting from ZENBU's SVG export. ![](http://population-transcriptomics.org/images/CAGEscan.png) ...
written 12 weeks ago by Charles Plessy2.3k

Latest awards to Charles Plessy

Scholar 15 days ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 15 days ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 4 months ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 5 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Good Answer 5 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Appreciated 5 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 5 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: why does this pipe work
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Scholar 7 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Scholar 7 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 7 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 7 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 7 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Appreciated 8 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 8 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.
Appreciated 9 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.

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