User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague4.7k
Reputation:
4,660
Status:
Trusted
Location:
Belgium
Last seen:
18 minutes ago
Joined:
4 years, 1 month ago
Email:
c**********@gmail.com

Posts by Carlo Yague

<prev • 595 results • page 1 of 60 • next >
0
votes
2
answers
135
views
2
answers
Comment: C: cutoff for expressed genes in DESeq2
... > it seems that rlog or vst normalized counts are recommended instead These are recommended when you need to compare gene expression between conditions. To see whether a gene is expressed within a single condition, RPKM/FPKM are fine IMHO. ...
written 14 days ago by Carlo Yague4.7k
0
votes
2
answers
814
views
2
answers
Comment: C: SSD or HHD for genome analysis
... Sure, not everything can be put on the SSD of hybrid drives because they have far more limited capacity than full SSD drives. In the context of bioinformatics, it could be worth it for, lets say, the scripts and libraries that are often accessed, small databases, perhaps the indexed genome for read ...
written 16 days ago by Carlo Yague4.7k
0
votes
2
answers
138
views
2
answers
Comment: C: Make a matrix from last coloumn of all files with different number of rows
... in R, you can use the `merge` function to merge dataframes based on, for instance, the Gene ID column. If you build a loop around that, you should be able to get what you want. ...
written 16 days ago by Carlo Yague4.7k
2
votes
0
answers
132
views
0
answers
Comment: C: Log2FC at 2 time point
... These are all very good points, but I would not be so definitive about the lack of replicate leading to *"no meaningful statistics"*. Actually, there is enough data here to build a statistical model of the form (expression ~ strain + time), without the interaction term (strain:time). In practice tho ...
written 16 days ago by Carlo Yague4.7k
1
vote
1
answer
152
views
1
answers
Comment: C: Count matrix from bigwig files - Application
... ATpoint raised important issues here and I tend to agree with him. That being said, [deeptools multiBigwigSummary][1] used with the options `--outRawCounts` and `--BED` (with a GTF file) can summarize read counts on exons from bigwig files. [1]: https://deeptools.readthedocs.io/en/develop/content ...
written 16 days ago by Carlo Yague4.7k
0
votes
2
answers
814
views
2
answers
Comment: C: SSD or HHD for genome analysis
... You could also consider [Hybrid drives][1]. I used to have one of those in the past and it felt like the best of both worlds to me: plenty of cheap storage with the HDD and speed with the SSD. [1]: https://en.wikipedia.org/wiki/Hybrid_drive ...
written 16 days ago by Carlo Yague4.7k
0
votes
0
answers
92
views
0
answers
Comment: C: Bam QC, GC content
... > Have you got some idea why GC content is so shifted? Here are some suggestions on where to dig to investigate the question: What are you sequencing exactly (species, tissue, ...) ? Do you expect any kind of contamination from different species (virus, bacteria, ...) ? Have you mapped to the tr ...
written 6 weeks ago by Carlo Yague4.7k
0
votes
1
answer
205
views
1
answers
Comment: C: Gene set enrichment analysis using a curated gene list and cluster DE genes
... > The odds ratio looks off in this case Why do you think this ? ...
written 3 months ago by Carlo Yague4.7k
0
votes
1
answer
205
views
1
answers
Comment: C: Gene set enrichment analysis using a curated gene list and cluster DE genes
... The hypergeometric test (urn problem) is equivalent to the corresponding one-tailed version of Fisher's exact test. It is just a different way to think about the data, as it provides the same pvalue. See with the OP's data: > fisher.test(matrix(c(209,5631,303,16857),2,2), alternative="g")$p. ...
written 3 months ago by Carlo Yague4.7k
1
vote
0
answers
141
views
0
answers
Comment: C: Is their a way to update HtSeq without uninstalling it?
... You could also try with pip if pip is installed. sudo pip install htseq --upgrade ...
written 3 months ago by Carlo Yague4.7k

Latest awards to Carlo Yague

Popular Question 7 days ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 5 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 7 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 input for DE analysis
Commentator 13 months ago, created a comment with at least 3 up-votes. For C: What is the purpose of running Cufflinks without a reference annotation?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 13 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 14 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 14 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 14 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 15 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Good Answer 16 months ago, created an answer that was upvoted at least 5 times. For A: The bed12 format
Scholar 17 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 19 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Scholar 19 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 20 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2033 users visited in the last hour