Moderator: seidel

gravatar for seidel
seidel6.2k
Reputation:
6,210
Status:
Trusted
Location:
United States
Scholar ID:
Google Scholar Page
Last seen:
6 days, 9 hours ago
Joined:
7 years, 6 months ago
Email:
c*******@gmail.com

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

Posts by seidel

<prev • 382 results • page 1 of 39 • next >
2
votes
1
answer
117
views
1
answers
Answer: A: Single-cell RNA seq
... Yes, you would use the hg19 fat sequence and gtf, to make an alignment index. But if you want your alignment results to contain values for the control spikes, they are saying that you'll have to supplement the hg19 reference and gtf with sequences and annotation for the control spikes. If you don't ...
written 7 days ago by seidel6.2k
0
votes
2
answers
231
views
2
answers
Answer: A: Transcription factor enrichment analysis
... You can use the edgeR or DESEQ2 packages to find differentially expressed genes from your RNA Seq data, and you can use the GenomicRanges package to slice and dice your ChIP Seq data (assuming you've called peaks). However, you'll have to be a lot more specific with your question to get more specifi ...
written 11 weeks ago by seidel6.2k
2
votes
3
answers
352
views
3
answers
Answer: A: Editing header of a fasta file
... If your field of interest is always in the same position, you can try awk with the split() function and do something like the following: awk '{split($0,a,":"); if(a[10]) print ">"a[10]; else print; }' yourfile.fasta > newfile.fasta This translates to: split the input line by semicolon an ...
written 3 months ago by seidel6.2k
1
vote
1
answer
218
views
1
answers
Comment: C: how to determine the controls for cnv
... You need to improve this question. There aren't nearly enough details to understand how to formulate an answer. What kind of cnv analysis are you doing? What tools might you try? What is the experimental set up? What is the experimental system? What organism? ...
written 4 months ago by seidel6.2k
0
votes
3
answers
3.1k
views
3
answers
Comment: C: How to annotate gene names for genomic coordinates?
... You mean instead of segments to genes, you want to know what genes appear within a given segment? The answer is above. Your cnv range (i.e. a segment) will return the index of the genes it overlaps. However, it can also be useful to turn the problem around, and use your genes as the query. i.e. for ...
written 4 months ago by seidel6.2k
1
vote
0
answers
295
views
0
answers
Comment: C: How to assign known subtype based on known gene signature
... What exactly is a subtype? Subtype of what? If I understand your question: you have three gene expression signatures - which means essentially that you have 3 vectors of numbers. You then have additional data. Each additional data set can be classified on whether or how well it matches any of the th ...
written 10 months ago by seidel6.2k
1
vote
4
answers
479
views
4
answers
Answer: A: How relevant, valuable, and important is Information Visualization nowadays in B
... Visualization can directly engage the decision making part of your brain, that is, *good* visualizations can. So from that perspective, a good visualization is essential. A picture that communicates a concept in data is very valuable, especially to the extent that it helps you *think* about that dat ...
written 10 months ago by seidel6.2k
2
votes
2
answers
540
views
2
answers
Answer: A: Visualizing hg19 and hg38 FPKMs in a single plot
... If you have FPKM values, then essentially the mapped reads have already been normalized to the appropriate gene structure, as Santosh notes in his comment "Note also that FPKM is normalized for transcript length". You can put them together in the same plot, but I would comment appropriately in the l ...
written 10 months ago by seidel6.2k
0
votes
2
answers
8.5k
views
2
answers
Comment: C: How To Extract Reads-Pairs Aligned Concordantly Exactly 1 Time?
... The -h simply tells samtools to print out the header as well as the reads. Thus if you were to pipe this into another bam file (by also using the -b option) you have a fully formed bam file. ...
written 18 months ago by seidel6.2k
0
votes
2
answers
510
views
2
answers
Answer: A: expression matrix from two dyes array
... You'll have to build your own matrix, extracting the value for that gene from each channel of the array. The problem with this, is one of normalization. You'd have to explore the difference between normalization the data as a two-channel array, then extracting out the normalized values, versus treat ...
written 19 months ago by seidel6.2k

Latest awards to seidel

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Scholar 12 weeks ago, created an answer that has been accepted. For A: genomicranges outside sequence bounds
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Appreciated 10 months ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Appreciated 16 months ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Good Answer 18 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 18 months ago, created an answer that was upvoted at least 5 times. For A: Entice Biologists To Learn R
Appreciated 18 months ago, created a post with more than 5 votes. For C: Tabular-To-Tab Delimited Conversion
Appreciated 18 months ago, created a post with more than 5 votes. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Appreciated 18 months ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Teacher 19 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Appreciated 21 months ago, created a post with more than 5 votes. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Appreciated 21 months ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Appreciated 21 months ago, created a post with more than 5 votes. For C: Tabular-To-Tab Delimited Conversion
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Appreciated 23 months ago, created a post with more than 5 votes. For A: Technical Or Biological Replicate
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: What Are The Softwares Can Be Used For Hierarchical Clustering?
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: How Does A Bioinformatics Scientist Document His/Her Work?
Teacher 24 months ago, created an answer with at least 3 up-votes. For A: Technical Or Biological Replicate
Good Answer 2.1 years ago, created an answer that was upvoted at least 5 times. For A: How Does A Bioinformatics Scientist Document His/Her Work?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 928 users visited in the last hour