User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague3.6k
Reputation:
3,570
Status:
Trusted
Location:
Belgium
Last seen:
16 hours ago
Joined:
2 years, 4 months ago
Email:
c**********@gmail.com

Posts by Carlo Yague

<prev • 486 results • page 1 of 49 • next >
0
votes
1
answer
124
views
1
answers
Comment: C: Why are DESeq2 size factors not null in case of sparse count matrix?
... Yes, the size factors can never be 0 because they are used to divide the read counts by genes. By the way, size factors are distributed around 1 and the mean of all size factors in your study is equal to 1. ...
written 4 days ago by Carlo Yague3.6k
0
votes
1
answer
124
views
1
answers
Comment: C: paired-end, single-end, polyA tail, 500bp, and removal of RNA genes
... Note that many lncRNAs are polyadenylated. ...
written 9 days ago by Carlo Yague3.6k
0
votes
1
answer
181
views
1
answers
Comment: C: What is the best method ChIPseq differential binding analysis?
... I can't tell you about the other tools, but ODIN doesn't take replicates into account, so you can cross this one from your list. THOR (from the same group) uses replicates and is a better option, especially if you have input controls. ...
written 12 days ago by Carlo Yague3.6k
1
vote
4
answers
381
views
4
answers
Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... > If the assumption is true, the above data should be essentially a line > because, at a given mean expression level, there is only one value for > the variance, isn't it As i.subery stated in its last comment below, this is more about folowing a trend than an exact relationship. Also, not ...
written 4 weeks ago by Carlo Yague3.6k
2
votes
3
answers
162
views
3
answers
Answer: C: Which aligment tool is best for eukaryotic transcriptome?
... You should also consider pseudo-alignments tools, such as [kallisto][1] and [salmon][2]. They are extremely fast and lightweight, can quantify millions of reads under a few minutes on a laptop computer. [1]: https://pachterlab.github.io/kallisto/about [2]: https://combine-lab.github.io/salmon ...
written 4 weeks ago by Carlo Yague3.6k
0
votes
4
answers
381
views
4
answers
Comment: C: Is it appropriate to assume genes of similar expression level also have similar
... IMO, the last plot kind of supports the relationship between the mean and standard deviation. See how the lower bound of standard deviation increases with the mean. Of course, for some genes, the standard deviation is much higher than the average trend. This is expected from biological data and it ...
written 4 weeks ago by Carlo Yague3.6k
1
vote
0
answers
161
views
0
answers
Comment: C: strand specific RNA-seq mapping for bacterial transcriptomics
... I wonder how you would define "best". Anyway, given how widely used they are, I would say that bowtie2 and BWA are solid choices for procaryotes. ...
written 5 weeks ago by Carlo Yague3.6k
0
votes
1
answer
117
views
1
answers
Answer: A: paired-end alignment with tophat2 expected (mean) inner distance between mate pa
... You can infer the mean inner distance between mates in different ways: **1. Experimental**: The inner distance depends directly on the fragments sizes of the cDNA library. This can be measured by running a bioanalyzer chip on it. You can then estimate the inner distance as `Inner_Dist = Fragment_ ...
written 5 weeks ago by Carlo Yague3.6k
2
votes
1
answer
113
views
1
answers
Answer: A: Retrieve coverage/depth of individual bed tracks from merged bed
... You can try [bedtools genomecov][1] : cat test.bed chr1 5 27 chr1 7 12 chr1 10 20 chr1 22 27 chr1 24 30 cat chr.txt chr1 50 bedtools genomecov -i test.bed -g chr.txt -bg chr1 5 7 1 chr1 7 10 2 chr1 10 12 3 chr1 12 20 2 chr1 20 22 1 ...
written 6 weeks ago by Carlo Yague3.6k
0
votes
1
answer
134
views
1
answers
Comment: C: Bowtie paired-end alignment failure
... From what I see, it looks like you are trying to map only one read, but you should also map its mate... what command did you use ? For paired-end data, it should looks like : bowtie2 -x *index* -1 *read* -2 *mate* ...
written 6 weeks ago by Carlo Yague3.6k

Latest awards to Carlo Yague

Scholar 5 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Intron-aware coverage for paired-end RNA-seq data.
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 10 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
Scholar 10 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 12 weeks ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 3 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 4 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 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 6 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 7 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 7 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 7 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 7 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 9 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 10 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 11 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 11 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 11 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 11 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 11 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 11 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 11 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: 1201 users visited in the last hour