User: Charles Plessy

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Charles Plessy2.3k
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Posts by Charles Plessy

<prev • 249 results • page 1 of 25 • next >
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Answer: A: What exactly is sequencing depth in RNAseq?
... *"how deep each sample was sequenced"* means *"how many reads (or pairs)" were sequenced for each sample*. Some results will vary with the number of sequenced reads (the *sequencing depth*), therefore it is an important information. ...
written 15 days ago by Charles Plessy2.3k
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Comment: C: The push toward standardisation
... Re-running a workflow (pipeline) after changing a single component is difficult when using pre-packaged software. For instance, a package with just the bug solved may not exist (instead, there may be an upgraded version where the bug was changed and in addition some algorithm modified). Perhaps wha ...
written 16 days ago by Charles Plessy2.3k
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Comment: C: Minimal TPM threshold for qPCR measure of gene expression
... You wrote « I want to find marker genes » in your original question. This is a hard problem that can not be summarised in a few lines, and that can not be solved by just picking a bunch of genes for making presence/absence calls. I recommend you to seek advice from somebody who has experience in t ...
written 16 days ago by Charles Plessy2.3k
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Comment: C: Minimal TPM threshold for qPCR measure of gene expression
... Yes, it is just an illustration that 0.1 TPM probably translates into "not a piece of cake" at the bench. ...
written 16 days ago by Charles Plessy2.3k
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Answer: A: Minimal TPM threshold for qPCR measure of gene expression
... For the sake of easy calculation, let's imagine that: - Detection threshold for PCR is 10 molecules (90 % loss); - Reverse-transcription is 1 % efficient (99% loss); Then to detect an expression level of 0.1 *transcript per millon*, one would need to load 1010 molecules in the RT-PCR. Let's ima ...
written 16 days ago by Charles Plessy2.3k
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Answer: A: The push toward standardisation
... I am not sure to understand that you are looking for, but you might find inspiration in large-scale software distributions like [Debian](https://www.debian.org) (which is obviously more than just that), where we have high aims on [software freedom](https://www.debian.org/social_contract), [community ...
written 16 days ago by Charles Plessy2.3k
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Answer: A: Help with Illumnina Headers
... See the option `-F | --origfmt` of [`fastq-dump`](https://ncbi.github.io/sra-tools/fastq-dump.html) to get the original sequence names. ...
written 17 days ago by Charles Plessy2.3k
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Answer: A: ERCC count matrix smart-seq2
... The [ERCC RNA spike-in mixes](https://www.thermofisher.com/order/catalog/product/4456740) manufactured by Thermo Fisher cover six orders of magnitude of concentrations, therefore it is expected by design that a large number of them will not be detected. You can have a look at [Svensson *et al.*, 20 ...
written 28 days ago by Charles Plessy2.3k
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Answer: A: Change list of consecutive genomic coordinates to intervals?
... With Bioconductor: > suppressPackageStartupMessages(library(GenomicRanges)) > reduce( GRanges( seqnames = c(1,1,1,1,1,1,8,8,8,8), ranges = IRanges( start = c(501,502,503,634,635,636,9982,9983,9984,9985), width ...
written 29 days ago by Charles Plessy2.3k
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Comment: C: Must there be spaces after "ORIGIN" in GenBank records ?
... Thanks Kevin for your kind offer (my gut feeling is that PaVE is wrong and genbankr is right) I added example data to the original post. ...
written 4 weeks ago by Charles Plessy2.3k

Latest awards to Charles Plessy

Scholar 16 days ago, created an answer that has been accepted. For A: Bedtools trouble with double digit chromosomes
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: fastq compression tools of choice
Teacher 27 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 10 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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