Moderator: seidel

gravatar for seidel
seidel6.8k
Reputation:
6,850
Status:
Trusted
Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
1 week ago
Joined:
9 years, 8 months ago
Email:
c*******@gmail.com

I work as a scientist at a non-profit research institute.

Posts by seidel

<prev • 409 results • page 1 of 41 • next >
0
votes
1
answer
101
views
1
answers
Comment: C: how to compare the difference of read counts in a given region
... Sorry about that. I updated the references. ...
written 15 days ago by seidel6.8k
1
vote
1
answer
63
views
1
answers
Answer: A: Euclidean Clustering and pattern confusion
... Your graphic is cut off - so we can only see what's happening in the top portion of your heat map - but assuming the pattern is preserved in the unseen portion, the simple answer is that the averages of the columns making up C3 are more similar to those of C2 and C4 than to C1, so the dendrogram was ...
written 15 days ago by seidel6.8k
0
votes
1
answer
101
views
1
answers
Answer: A: how to compare the difference of read counts in a given region
... The simplest answer would be to use the Poisson distribution. Assuming your data is normalized for read depth, you have a background estimate for your window of interest (lambda = 50), and an observed count for that window in your IP (1000), so in R you could estimate this with: ppois(100, lamb ...
written 18 days ago by seidel6.8k
1
vote
0
answers
270
views
0
answers
Comment: C: How to create custom gtf annotation file?
... Can't you just grep for the gene name of interest and redirect the output to a file? All the lines relevant to that gene should have the ID, and this would select and place all lines with the given gene id into a single file. ...
written 3 months ago by seidel6.8k
0
votes
3
answers
315
views
3
answers
Comment: C: Can I compare TPM values for a transcript across different transcriptome assembl
... Yes...assuming the same set of transcripts is quantified between experiments, and the the non-zero count transcripts are identical between sets (i.e. the set of "expressed" transcripts is the same between conditions). In the case above, we both both different conditions AND different transcriptomes. ...
written 3 months ago by seidel6.8k
0
votes
2
answers
536
views
2
answers
Comment: C: Seeking for a Linux based script ?
... You want to convert "15:" to ">"? Or in general, do you want to convert anything to the left of the colon, including the colon, to ">"? For any number of lines in a file? There are ways to do both. One could easily use sed, or awk, or perl, with a one-liner (so no real script required), but as ...
written 9 months ago by seidel6.8k
7
votes
3
answers
1.7k
views
3
answers
Answer: A: Reproducing this plot in R
... Something like the following would work with base R functions: # make some data a <- data.frame(sample=paste0("A", 1:50), log10_total_counts=rnorm(50, 6)) # get x points x <- 1:length(a$log10_total_counts) # create plot, drop x axis plot(x, a$log10_total_cou ...
written 9 months ago by seidel6.8k
2
votes
2
answers
1.3k
views
2
answers
Answer: A: Creating Count Matrix
... One suggestion using R would be: # only return file names with a given pattern dir(pattern="ReadsPerGene.out.tab") # save the results to a variable files <- dir(pattern="ReadsPerGene.out.tab") counts <- c() for( i in seq_along(files) ){ x <- read.tab ...
written 9 months ago by seidel6.8k
0
votes
2
answers
1.3k
views
2
answers
Comment: C: Creating Count Matrix
... What language/method would you like to use? This can be done using shell, R, python, perl, etc.....you name it. What are you familiar with? ...
written 9 months ago by seidel6.8k
0
votes
0
answers
388
views
0
answers
Comment: C: RNA-Seq Differential gene expression
... One straightforward approach would be to use STAR to generate a count table that you can use with edgeR. Look up the edgeR userguide - it has a rich description of how to quantify differential gene expression given various experimental designs. ...
written 10 months ago by seidel6.8k

Latest awards to seidel

Scholar 8 weeks ago, created an answer that has been accepted. For A: Concatenate mutiple samples from tophat to run cuffdiff
Scholar 8 weeks ago, created an answer that has been accepted. For A: genomicranges outside sequence bounds
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Appreciated 8 months ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Good Answer 9 months ago, created an answer that was upvoted at least 5 times. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Appreciated 9 months ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Scholar 9 months ago, created an answer that has been accepted. For A: genomicranges outside sequence bounds
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Popular Question 19 months ago, created a question with more than 1,000 views. For Archiving BAM files and analysis
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Appreciated 19 months ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Teacher 20 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: Experimental Techniques To Measure Protein-Protein And Protein-Ligand Structure
Appreciated 2.2 years ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Scholar 2.2 years ago, created an answer that has been accepted. For A: genomicranges outside sequence bounds
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Good Answer 2.2 years ago, created an answer that was upvoted at least 5 times. For A: Entice Biologists To Learn R
Commentator 2.3 years ago, created a comment with at least 3 up-votes. For C: Experimental Techniques To Measure Protein-Protein And Protein-Ligand Structure
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Scholar 2.4 years ago, created an answer that has been accepted. For A: genomicranges outside sequence bounds
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Teacher 2.9 years ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 2259 users visited in the last hour