User: tlorin

gravatar for tlorin
tlorin150
Reputation:
150
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Trusted
Location:
Switzerland
Last seen:
2 days, 6 hours ago
Joined:
2 years, 2 months ago
Email:
t***************@orange.fr

Posts by tlorin

<prev • 36 results • page 1 of 4 • next >
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Comment: C: Mapping RNA-Seq data on genome from another species
... Thanks Brian! If I add `maxindel=200k minid=0.7` do I risk mapping to spurious locations or will the mapping report the best unique hit (so, the homologous sequence in my case)? ...
written 7 days ago by tlorin150
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Comment: C: Mapping RNA-Seq data on genome from another species
... Thanks for your answer! But why `--outFilterMismatchNmax 8`and not `--outFilterMismatchNmax 15` or over threshold? Is this some arbitrary threshold that you found was best? I guess this depends on the evolutionary distance between both species too. Is [this][1] the post you refer to? [1]: https: ...
written 8 days ago by tlorin150
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Mapping RNA-Seq data on genome from another species
... Hello all, I have RNA-Seq data from a species **A** for which I don't have a reference genome. I would like to map this data on the closest available genome from species **B**. I have read [this post][1] and I am planning to use `hisat2` or `STAR`. Does any of you have recommandations regarding t ...
genome hisat2 star rna-seq mapping written 8 days ago by tlorin150 • updated 8 days ago by Brian Bushnell11k
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Comment: C: Fasta to gff with custom set of genes
... `I don't agree completely. If your reads are RNASeq reads and you map them against a transcriptome, it shouldn't be a problem.` Definitely! Was just saying that you have to map your reads to a whole genome or transcriptome, not to "simply" 100 or 200 genes. ...
written 5 weeks ago by tlorin150
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Fasta to gff with custom set of genes
... Dear all, I have a custom list of 100 genes that I manually curated to obtain the full CDS and I would like to make differential expression (DE) analysis between samples for this very subset. I now I cannot simply map all the reads onto this subset and perform DE analysis because I would have [norm ...
fasta genome gff deseq2 rna-seq written 5 weeks ago by tlorin150 • updated 5 weeks ago by Macspider1.1k
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Comment: C: Why the local blast and online blast produce different results?
... Thanks for this solution @Juke-34. Indeed, the command line default parameter for `blastn` is 28, whereas the online default parameter is 11... ...
written 4 months ago by tlorin150
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Comment: C: Understanding NCBI identifiers
... I know that nr is supposed to be non-redundant (that's why I use it), but then why are there only 2 hits left (NP_001133180.1 and NP_001133181.1) when we blast the sequence onto the RefSeq database? Which one should I trust 'in general'? It seems to be that everyone has a 'feeling' about this but I ...
written 8 months ago by tlorin150
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Understanding NCBI identifiers
... This is kind of a general question regarding NCBI accesion numbers. Suppose I have this sequence >myseq MGQ-----NSPNLLR------LSQ --TLVGSSLLSSPSSPTTLKVKMPHAFPFLTPDQ-KKELSDIAHKIVAKGKGILAADES- --TGSVAKRFQSINTENTEENRRLYRQLLFTA-DERAGPCIGGVIFFHETLYQKTDAGKT FPEHVKSRGWVVGIKVDKGVVPLA ...
ncbi id written 8 months ago by tlorin150
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Comment: C: RepeatModeler cannot be run in parallel
... Haha I checked and I did install version 1.0.8 :) ...
written 8 months ago by tlorin150
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RepeatModeler cannot be run in parallel
... Dear all, I am trying to run RepeatModeler with multiple processors with the `-pa` option. I downloaded RepeatModeler (last version available [here][1]) and installed it properly (it runs perfectly but for a reaaaaaaaaaaaally long time). The documentation [here][2] and [here][3] says that I shoul ...
repeatmodeler repeatmasker written 8 months ago by tlorin150 • updated 5 weeks ago by cristina.osuna.cruz0

Latest awards to tlorin

Voter 28 days ago, voted more than 100 times.
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: Tajima's D value interpretation
Appreciated 7 months ago, created a post with more than 5 votes. For A: Tajima's D value interpretation
Popular Question 8 months ago, created a question with more than 1,000 views. For Fasta to axt - KaKs Calculator
Popular Question 18 months ago, created a question with more than 1,000 views. For Heatmap with categorical variables and with phylogenetic tree in R or Python
Scholar 18 months ago, created an answer that has been accepted. For A: Heatmap with categorical variables and with phylogenetic tree in R or Python
Supporter 20 months ago, voted at least 25 times.
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Heatmap with categorical variables and with phylogenetic tree in R or Python
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Heatmap with categorical variables and with phylogenetic tree in R or Python
Scholar 2.2 years ago, created an answer that has been accepted. For A: Heatmap with categorical variables and with phylogenetic tree in R or Python

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