User: Carlo Yague

gravatar for Carlo Yague
Carlo Yague4.9k
Reputation:
4,920
Status:
Trusted
Location:
Canada
Last seen:
17 hours ago
Joined:
4 years, 6 months ago
Email:
c**********@gmail.com

Posts by Carlo Yague

<prev • 619 results • page 1 of 62 • next >
1
vote
3
answers
107
views
3
answers
Answer: C: How to blastn a very short query sequence? Identifying telomeres in assembly
... If you are looking for exact repeats of at least n TTAGGG, you could just perhaps just use grep. ...
written 29 days ago by Carlo Yague4.9k
0
votes
3
answers
107
views
3
answers
Comment: C: How to blastn a very short query sequence? Identifying telomeres in assembly
... The minimal seed length is 7 for blast actually. Still too much for this, unless you blast on two or more tandem repeats. For instance: >query sequence TTAGGGTTAGGGTTAGGG ...
written 29 days ago by Carlo Yague4.9k
1
vote
3
answers
102
views
3
answers
Comment: C: Bedtools intersect/bcftools annotate dublicate the SNPs
... I can see that the gene is the same after you use bcftools annotate, but is it the same using bedtools interesct -wa -wb ? It shouldn't be the same then. ...
written 29 days ago by Carlo Yague4.9k
1
vote
3
answers
102
views
3
answers
Answer: A: Bedtools intersect/bcftools annotate dublicate the SNPs
... Could it be that some SNP fall onto multiple genes ? Because of overlapping genes or sense/antisense gene pairs. To check this, I would just look at the output of intersect -a {input.invcf} -b {input.bedgz} -header -wa -wb > out.bed where the option -wb ensure that the full gene entry of ` ...
written 4 weeks ago by Carlo Yague4.9k
0
votes
2
answers
101
views
2
answers
Answer: A: Removing outliers from bigwig files
... How do you define outliers ? regions with high coverage ? If you were to filter out those regions, then you might remove bound regions (if we talk about ChIP-seq) or other regions of interest. So I do not think this is a good strategy. Alternatively, you might: 1. *[quickfix]* Use a fixed y ...
written 4 weeks ago by Carlo Yague4.9k
0
votes
1
answer
110
views
1
answers
Comment: C: PCR duplicate reads - samtools
... To make it clear, the "+ 0" on every line refer to the number of Qc-failed reads in each category. And the number to the left of the "+" always refer to Qc-passed reads. ...
written 5 weeks ago by Carlo Yague4.9k
0
votes
0
answers
133
views
0
answers
Comment: C: Combining two BED files based on shared criteria
... so what do you mean by this *"For some of the intervals in the first set there are multiple single bp foci in the second set and I would like that represented in the final 4 column interval."* ? ...
written 4 months ago by Carlo Yague4.9k
2
votes
0
answers
239
views
0
answers
Comment: C: DESeq2 design and Batch effects
... For me, the most important point is to NOT define sample groups according to the expression data (PCA, etc). The design of the experiment should be set before, according to the... hum... design of the experiment. It should never be set *a posteriori*. So when you say: > Another possibility that ...
written 4 months ago by Carlo Yague4.9k
1
vote
1
answer
111
views
1
answers
Answer: A: Input for DESEQ2 (after featurecounts)
... > Now i should go to DEseq2, but do i need one file with all my samples, > or is it possible to go to DEseq2 with each sample separated? Both are possible, but the easiest is to run featureCounts on all your samples at the same time: all_sample_counts = featureCounts(files=c("H1_1sorted. ...
written 4 months ago by Carlo Yague4.9k
0
votes
1
answer
153
views
1
answers
Comment: C: Tophat2 RNA seq mapping
... nice catch ! alternatively: tophat -p 8 /scratch/sbag/Tikshana/Ath/index/Bowtie_Ath/Bowtie_Ath -o /scratch/sbag/Tikshana/Ath/map/Athctrl_tophat/genome /scratch/sbag/Tikshana/Ath/Athctrl_1P.fastq /scratch/sbag/Tikshana/Ath/Athctrl_2P.fastq ...
written 4 months ago by Carlo Yague4.9k

Latest awards to Carlo Yague

Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: how to get p value for a set of fdr value
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?
Appreciated 3 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
Scholar 3 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 4 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Appreciated 4 months ago, created a post with more than 5 votes. For A: DESeq2 proper design setting
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
Popular Question 5 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Commentator 8 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 10 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 10 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 12 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
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
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: DESeq2 input for DE analysis
Commentator 18 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 19 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Teacher 19 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 19 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 19 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Scholar 19 months ago, created an answer that has been accepted. For A: cufflinks with reference annotation, FPKM for a gene
Popular Question 20 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Popular Question 20 months ago, created a question with more than 1,000 views. For Splicing-defect analysis with RNA-seq paired-end data
Good Answer 22 months ago, created an answer that was upvoted at least 5 times. For A: The bed12 format

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1126 users visited in the last hour