User: Charles Plessy

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Charles Plessy1.6k
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Japan
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2 years, 8 months ago
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Posts by Charles Plessy

<prev • 192 results • page 1 of 20 • next >
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Answer: A: TSS for lncRNAs from GENCODE
... If it is not too late, have a look at the "[FANTOM CAT](http://fantom.gsc.riken.jp/cat)", which is *"an atlas of human long non-coding RNAs with accurate 5′ ends"*. ...
written 3 days ago by Charles Plessy1.6k
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Answer: A: Help, I'm having problem with bwa mapping
... You have to create a BWA index containing *"the hg19 reference genome plus exonic sequences surrounding all currently known splicing junctions from gene models available in annotation from Gencode, RefSeq, Ensembl and UCSC Genes"*. If the authors did not leave a more detailed description of the con ...
written 3 days ago by Charles Plessy1.6k
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Comment: C: trimming reads in fastq file
... (I just answered in the post that you linked) ...
written 3 days ago by Charles Plessy1.6k
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Answer: A: Mismatch on first base gives wrong TSS
... Hi Chirag, on my side, I usually work on the CAGE data after it is transformed to a BED format, and during that transformation I apply a naive correction for the extra Gs. My workflow is paired-end, so it does not directly apply to the modENCODE data, but for the sake of the example, here is an ex ...
written 3 days ago by Charles Plessy1.6k
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Comment: A: Are micro-first exons in GENCODE26 real ?
... Thanks Mark for the detailed answer. And thanks as well to Sanger's help desks who also always gave me prompt and detailed answers. I hope that this discussion on Biostars can be useful to others, which is why I opened it in parallel. Back to 5′ ends, is there a way to infer from GENCODE's GFF fi ...
written 3 days ago by Charles Plessy1.6k
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Comment: C: SciClone installation in R version 3.3.3
... > sudo rm -r /tmp/* Be careful: on a multi-user platform, one will annoy many people with such a command, and even on your own computer you can shoot yourself in the foot if you were running other programs at the same time. I do not see this command being discussed in other answers. Are you su ...
written 3 days ago by Charles Plessy1.6k
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Answer: A: StackExchange/Area51 bioinformatics is back
... [Biostars's engine](https://github.com/ialbert/biostar-central) is is [Free software](https://github.com/ialbert/biostar-central/blob/master/LICENSE.txt) while [StackExchange's engine is proprietary](https://meta.stackexchange.com/questions/14656/is-the-stack-overflow-source-code-available). Given ...
written 4 days ago by Charles Plessy1.6k
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Answer: A: Generate column names on the fly R
... The format of your file looks like the [Order Switchable Column Table](https://sourceforge.net/projects/osctf/) (OSCT) format, but this format requires that *"the first line after the comments/meta-data (see below) is a header line, which indicate column names of the table"*. If the OSCT format was ...
written 4 days ago by Charles Plessy1.6k
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Answer: A: trimming reads in fastq file
... You can use [EMBOSS](http://emboss.sourceforge.net/) to trim the first base of [sequences in many formats](http://emboss.sourceforge.net/docs/themes/SequenceFormats.html#mult), including FASTQ. In the example below, I saved your sequenced in a file names `toto.fq`. As you can see, EMBOSS discards ...
written 5 days ago by Charles Plessy1.6k
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Comment: C: How to analyze CAGE-Seq data?
... For paired-end data my favourite approach is to convert paired alignments from BAM format, where each mate is represented on separate lines, to BED12 format, where each pair is on one line, using the [pairedBamToBed12](https://www.biostars.org/p/160342/) tool. The 5′ end of the BED entries is the CA ...
written 8 days ago by Charles Plessy1.6k

Latest awards to Charles Plessy

Scholar 1 day ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Scholar 2 days ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 2 days ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 3 days ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 4 days ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 22 days ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 22 days ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Appreciated 6 weeks ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Patch ERCC spike sequences to get their real 5-prime ends.
Appreciated 12 weeks ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Develop an R package for CRAN vs BioConductor
Appreciated 3 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Scholar 3 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
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Teacher 3 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Appreciated 3 months ago, created a post with more than 5 votes. For Patch ERCC spike sequences to get their real 5-prime ends.
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Scholar 4 months ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Scholar 4 months ago, created an answer that has been accepted. For A: Map human cell line RNA-seq data to virus
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