Moderator: rpolicastro
rpolicastro ♦ 3.3k
- Reputation:
- 3,340
- Status:
- Trusted
- Location:
- Bloomington, IN
- Website:
- https://www.linkedin.c...
- Twitter:
- rpolicas
- Scholar ID:
- Google Scholar Page
- Last seen:
- 5 hours ago
- Joined:
- 6 months, 1 week ago
- Email:
- r*************@gmail.com
Posts by rpolicastro
<prev
• 433 results •
page 1 of 44 •
next >
2
votes
1
answer
92
views
1
answers
... PCR amplification is common in both RNA-seq and scRNA-seq. The prevalence of duplicates in your sequenced library will be a function of library complexity (quantity of unique cDNAs before amplification) and sequencing depth. In general, the more complex the library, the deeper the library can be seq ...
written 8 hours ago by
rpolicastro ♦ 3.3k
1
vote
0
answers
94
views
0
answers
... By detect do you mean that you want to quantify reads associated with that transcript? If so, I would recommend using a program such as [Salmon](https://salmon.readthedocs.io/en/latest/salmon.html) to quantify transcripts. It builds an index using a fasta file of transcript sequences, so all you wou ...
written 10 hours ago by
rpolicastro ♦ 3.3k
0
votes
1
answer
103
views
1
answers
Comment:
C: Bioinformatics questions sequence
... The first question is asking to write a regular expression that captures those sequences. Depending on what language you are writing this in there will be regex tutorials that you should go through. ...
written 16 hours ago by
rpolicastro ♦ 3.3k
0
votes
1
answer
51
views
1
answers
... You seem to be pointing to a salmon transcriptome index instead of a STAR genome index. ...
written 20 hours ago by
rpolicastro ♦ 3.3k
0
votes
0
answers
35
views
0
answers
Comment:
C: Merging integrated datasets
... What strange results was the analysis giving? ...
written 21 hours ago by
rpolicastro ♦ 3.3k
1
vote
2
answers
79
views
2
answers
... Do the sequences match exactly? Also, is there any match in the names? ...
written 1 day ago by
rpolicastro ♦ 3.3k
5
votes
2
answers
669
views
2
answers
Answer:
A: Single cell RNA-seq anlaysis
... Since this post has accumulated views, I'll add a few resources.
I would consider the three most popular scRNA-seq frameworks to be [Seurat](https://satijalab.org/seurat/) (R), [Bioconductor](http://bioconductor.org/books/release/OSCA/) (R), and [Scanpy](https://scanpy.readthedocs.io/en/stable/) (P ...
written 1 day ago by
rpolicastro ♦ 3.3k
0
votes
0
answers
71
views
0
answers
Comment:
C: Ratio of Log2FC
... This seems like a poor (fatal) experimental design at first glance. Since protein and injection amount are perfectly correlated, you won't be able to deconvolute the effect of protein from injection amount. What was the reasoning behind injecting different amounts? ...
written 1 day ago by
rpolicastro ♦ 3.3k
0
votes
0
answers
190
views
0
answers
... Assuming Cell Ranger worked correctly, it likely means few cells were actually captured by the Chromium, and those few cells were over-sequenced by a factor of 100. Since it's likely an experimental error, you would need to consult with the people that loaded the cells. ...
written 4 days ago by
rpolicastro ♦ 3.3k
0
votes
0
answers
66
views
0
answers
... Can you include some example data, and an example of what you want the output to look like? ...
written 4 days ago by
rpolicastro ♦ 3.3k
Latest awards to rpolicastro
Teacher
1 day ago,
created an answer with at least 3 up-votes.
For A: HELP: Excel Index & Match in R - How to do it?
Teacher
1 day ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Teacher
2 days ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Scholar
6 days ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Scholar
14 days ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Scholar
16 days ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Voter
16 days ago,
voted more than 100 times.
Commentator
19 days ago,
created a comment with at least 3 up-votes.
For C: Am I crazy, or are most published RNA-seq studies vastly underpowered?
Teacher
19 days ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Scholar
19 days ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Scholar
20 days ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Commentator
21 days ago,
created a comment with at least 3 up-votes.
For C: Am I crazy, or are most published RNA-seq studies vastly underpowered?
Teacher
5 weeks ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Scholar
5 weeks ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Scholar
6 weeks ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Teacher
6 weeks ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Teacher
10 weeks ago,
created an answer with at least 3 up-votes.
For A: How to add column to table with awk
Scholar
10 weeks ago,
created an answer that has been accepted.
For A: How to add column to table with awk
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 2451 users visited in the last hour