User: Jason

gravatar for Jason
Jason890
Reputation:
890
Status:
Trusted
Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
11 months, 3 weeks ago
Joined:
9 years, 8 months ago
Email:
j***************@gmail.com

Posts by Jason

<prev • 66 results • page 1 of 7 • next >
1
vote
1
answer
339
views
1
answers
Comment: C: Same data, very different heatmaps
... I think you may want to first merge the data from each output in the same image so you can be confident how each gene is affected. Also, just some thoughts, you may want to look at the output values from each pipeline. See why they are different, maybe one is normalized in one way in which the other ...
written 3.5 years ago by Jason890
1
vote
4
answers
5.8k
views
4
answers
Comment: C: How to remove poly T in RNA-sequencing data
... Have you tried mapping the RNA-seq data yet? It may not be necessary to remove polyA stretches because they won't map to a unique location and you may already have enough reads to not worry about it. Another poster asked a similar question https://www.biostars.org/p/76891/ . However there are other ...
written 4.0 years ago by Jason890
0
votes
1
answer
1.7k
views
1
answers
Answer: A: Solid / Colorspace with bowtie : ERRO -> Extra parameter(s) specified
... You might want to try using /mm9IndexColor/m_musculus_ncbi37_c instead, I think bowtie recognizes the other files without the *.  I work in yeast and I have saccer2_R61-1-1.1.ebwt, saccer2_R61-1-1.2.ebwt etc in my directory but I only use  bowtie -f -C -S  saccer2_R61-1-1 in_F3.csfasta > out_F3 ...
written 4.0 years ago by Jason890
0
votes
1
answer
2.8k
views
1
answers
Comment: C: Can differential gene expression heatmaps be compared across multiple separate e
... Maybe if you made sure the colors were exactly the same (i.e. -1 log2FC = green and +1 = red) it would be at least relatively interpretable in a qualitative sense. Without merging them all together it might be difficult to determine if the same genes are illustrating the same patterns.  ...
written 4.5 years ago by Jason890
0
votes
1
answer
2.8k
views
1
answers
Answer: A: Can differential gene expression heatmaps be compared across multiple separate e
... I would merge the data into the same heatmap. If you have a sample that was included in both the RNA-seq from a year ago and the more recent run you should compare those first to see what the batch to batch variation is like. If they are very similar (R^2 > 0.9) then maybe you can just go ahead j ...
written 4.5 years ago by Jason890
1
vote
1
answer
4.5k
views
1
answer
RNA-seq: Adjust library size using total uniquely mappable tags or only reads that map to genes analyzed?
...   Hello,  I'm using edgeR to analyze RNA-seq data and I have a question about library size adjustment. There are essentially two ways to adjust the output for the differences in library sizes between each of the RNA-seq samples. One is to only use counts that are from genes, which are in the R mat ...
rna-seq edger written 4.5 years ago by Jason890 • updated 4.5 years ago by Devon Ryan90k
1
vote
4
answers
5.2k
views
4
answers
Answer: A: Ribo-seq Analysis software
... I would definitely talk with Dr. Edward O'Brien.  http://www.chem.psu.edu/directory/epo2 I've seen him give multiple talks on ribo-seq analysis here at PSU and he seems like he's very knowledgeable on the subject.  ...
written 4.7 years ago by Jason890
0
votes
2
answers
5.1k
views
2
answers
Comment: C: How can merge RNA-Seq biological replicates ?
... I second the concern about merging biological replicates. The purpose of performing biological reps is to measure variability between your samples. You need to at least show there is reasonably low variability between the replicates before merging them. You could calculate Pearson or Spearman values ...
written 4.7 years ago by Jason890
1
vote
2
answers
16k
views
2
answers
Comment: C: Scatter Plot For Correlations With Heatdensity
... I don't know exactly how to do that but maybe the contour function will help.  I asked a developer of LSD (Bjoern Schwalb), who actually posts a decent amount here, about what the values along the contour mean (see add.contour = TRUE) and he told me "the values shown are density estimates from a 2D ...
written 4.7 years ago by Jason890
1
vote
1
answer
7.8k
views
1
answers
Comment: C: what is enrichment of a chip-seq experiment
... Sounds good to me.  ...
written 4.8 years ago by Jason890

Latest awards to Jason

Great Question 21 months ago, created a question with more than 5,000 views. For How Do I Count The Number Values Less Than X In A Column Using R ?
Popular Question 21 months ago, created a question with more than 1,000 views. For How Do I Match Orthologues In One Species To Another, Genome Scale?
Good Answer 2.6 years ago, created an answer that was upvoted at least 5 times. For A: How Much Do You Trust Geneontology Annotations?
Appreciated 2.7 years ago, created a post with more than 5 votes. For A: How Much Do You Trust Geneontology Annotations?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Rip-Seq: How Do You Determine What'S Good Coverage?
Good Answer 3.2 years ago, created an answer that was upvoted at least 5 times. For A: How Much Do You Trust Geneontology Annotations?
Appreciated 3.3 years ago, created a post with more than 5 votes. For A: Scatter Plot For Correlations With Heatdensity
Epic Question 4.4 years ago, created a question with more than 10,000 views. For How Do I Count The Number Values Less Than X In A Column Using R ?
Voter 4.5 years ago, voted more than 100 times.
Popular Question 4.5 years ago, created a question with more than 1,000 views. For How Do I Match Orthologues In One Species To Another, Genome Scale?
Appreciated 4.7 years ago, created a post with more than 5 votes. For A: How Much Do You Trust Geneontology Annotations?
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: What Does Up-Regulated And Down-Regulated Mean?
Scholar 4.8 years ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Teacher 4.8 years ago, created an answer with at least 3 up-votes. For A: What Does Up-Regulated And Down-Regulated Mean?
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: What Does Up-Regulated And Down-Regulated Mean?
Scholar 5.1 years ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Teacher 5.1 years ago, created an answer with at least 3 up-votes. For A: What Does Up-Regulated And Down-Regulated Mean?
Great Question 5.1 years ago, created a question with more than 5,000 views. For How Do I Count The Number Values Less Than X In A Column Using R ?
Scholar 5.1 years ago, created an answer that has been accepted. For A: Overlaid XY plot with two different colors for control and target genes
Appreciated 5.2 years ago, created a post with more than 5 votes. For A: How Much Do You Trust Geneontology Annotations?
Appreciated 5.2 years ago, created a post with more than 5 votes. For How Do I Match Orthologues In One Species To Another, Genome Scale?
Appreciated 5.2 years ago, created a post with more than 5 votes. For How Do I Map, Align, And Plot My Solid Results?
Good Question 5.2 years ago, asked a question that was upvoted at least 5 times. For How Do I Match Orthologues In One Species To Another, Genome Scale?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2021 users visited in the last hour