User: Corentin

gravatar for Corentin
Corentin130
Reputation:
130
Status:
Trusted
Location:
Last seen:
2 days, 12 hours ago
Joined:
1 year, 1 month ago
Email:
c***************@gmail.com

Posts by Corentin

<prev • 14 results • page 1 of 2 • next >
0
votes
1
answer
84
views
1
answers
Comment: C: Platanus only use single thread
... Yes, that what I expected. But I was just thinking that the de Bruijn graph construction would be parallelized, maybe it is not implemented yet. ...
written 20 days ago by Corentin130
1
vote
1
answer
84
views
1
answer
Platanus only use single thread
... Hi, I am currently trying to assemble a heterozygous plant genome (estimated size 1 Gbp). I wanted to try "Platanus" (http://platanus.bio.titech.ac.jp/), I launched the "Platanus assemble" command with 80 threads, but now, at the "connecting kmers..." step it only uses one. It has run for several ...
assembly performance platanus written 23 days ago by Corentin130 • updated 23 days ago by colindaven640
1
vote
2
answers
235
views
2
answers
Comment: C: New Aligner Tool - Would you be interested in this ?
... This is an interesting idea, However, there is a tool doing something similar: http://teaser.cibiv.univie.ac.at/, have you checked it ? ...
written 6 weeks ago by Corentin130
2
votes
1
answer
118
views
1
answers
Answer: A: differential expression analysis of microarray data using limma package
... Hi, It seems alright, I think it would be informative to add some quality control at the beginning, you can do boxplots of the raw intensity to compare different cells, and check the RNA degradation with "AffyRNAdeg". If the quality seems not good enough for your analysis, you can them perform no ...
written 6 weeks ago by Corentin130
0
votes
1
answer
581
views
1
answers
Comment: C: Download SNPs data
... You can also look at the R package "gwascat": https://bioconductor.org/packages/3.7/bioc/vignettes/gwascat/inst/doc/gwascat.pdf which allows you to access and work with the National Human Genome Research Institute GWAS catalog. ...
written 6 weeks ago by Corentin130
0
votes
1
answer
568
views
1
answers
Comment: C: Pilon polish draft assembly, but it didn't work
... If you have time you can try to map with the -M option only, and then with the -P option only, to see which one of the two (or the two together) is causing the issue. I remember that for pilon the bams need to be "sorted in coordinate order and indexed" (https://github.com/broadinstitute/pilon/wiki ...
written 5 months ago by Corentin130
0
votes
1
answer
568
views
1
answers
Comment: C: Pilon polish draft assembly, but it didn't work
... Hi, did you checked your bam file ? You can run "samtools flagstat" on it to check the number of reads mapped to the reference. ...
written 6 months ago by Corentin130
5
votes
1
answer
420
views
1
answers
Answer: A: Selecting fastq sequences
... Hi, Your barcode variable is a *file object* and so an *iterator* (source: https://docs.python.org/2/library/stdtypes.html#bltin-file-objects **A file object is its own iterator** and https://stackoverflow.com/questions/16994552/is-file-object-in-python-an-iterable), when you loop through a file ob ...
written 6 months ago by Corentin130
0
votes
1
answer
855
views
1
answers
Answer: A: Data for drawing Heatmaps (RNA-seq)
... Hi, The normalization should be performed by the tool you are using (the most popular being EdgeR, DESeq2 and limma), each one of them has a different way of normalizing the data, but if your data is robust (one of the important thing is having enough replicates), they should give similar results, ...
written 7 months ago by Corentin130
0
votes
3
answers
1.1k
views
3
answers
Comment: C: Help! How to plot RNASeq data in PCA
... As an alternative to PCA you can also try MDS plots : https://www.rdocumentation.org/packages/edgeR/versions/3.14.0/topics/plotMDS.DGEList but it should give similar results ...
written 8 months ago by Corentin130

Latest awards to Corentin

Appreciated 6 months ago, created a post with more than 5 votes. For A: Selecting fastq sequences
Scholar 6 months ago, created an answer that has been accepted. For A: expression to networking
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: expression to networking
Scholar 9 months ago, created an answer that has been accepted. For A: expression to networking
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: expression to networking

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 991 users visited in the last hour