Moderator: ATpoint
ATpoint ♦ 26k
- Reputation:
- 25,570
- Status:
- Trusted
- Location:
- Germany
- Last seen:
- 6 hours ago
- Joined:
- 3 years, 7 months ago
- Email:
- a*********@gmail.com
Posts by ATpoint
<prev
• 3,511 results •
page 1 of 352 •
next >
0
votes
0
answers
52
views
0
answers
... Did you try sorting (no matter if you think it is or is not) sorted using `samtools` a representative BAM file and then try `stringtie` again? Did that work? Also please show the command that was used for sorting in the first place.
...
written 10 hours ago by
ATpoint ♦ 26k
0
votes
1
answer
693
views
1
answers
... How high is it? As often there is no fixed cutoff. ...
written 11 hours ago by
ATpoint ♦ 26k
0
votes
1
answer
143
views
1
answers
Comment:
C: RPKM with bowtie output
... Please read the manual and then come back with more specific questions while opening a new question, providing the necessary details. ...
written 14 hours ago by
ATpoint ♦ 26k
1
vote
1
answer
94
views
1
answers
... I strongly recommend that https://www.biostars.org/u/1987/ spends time on the basics of sequencing platforms and applications before making any business decisions on what kit/platform/strategy to use for the project. ...
written 15 hours ago by
ATpoint ♦ 26k
1
vote
1
answer
37
views
1
answers
Answer:
A: bbmap reference mapping error
... > The index format has changed in this version of BBTools. Please delete the /ref/ directory and re-index from the reference fasta.
Please read the error messages. It is clear what you have to do => re-index the genome if you want to stick with that version of the tool or use an older versio ...
written 17 hours ago by
ATpoint ♦ 26k
1
vote
1
answer
94
views
1
answers
... Adding on this, you should (and probably must) also choose between short and long read sequencing. As https://www.biostars.org/u/24526/ says some structural variants will be difficult or impossible to find with short reads whereas SNPs are the realm of short reads. ...
written 17 hours ago by
ATpoint ♦ 26k
1
vote
1
answer
100
views
1
answers
... Are these tumors which undergo (so the cells of origin) SHM? So essentially are these B-cell tumors? Can you also give some basic information about the treatment? Is it something that could activate an immune response? How early after the treatment have the specimen been collected? ...
written 1 day ago by
ATpoint ♦ 26k
0
votes
1
answer
80
views
1
answers
... What is `Invitro`? qPCR? Please add details: How many replicates, what is the setup, does PCA indicate good reproducability between replicates? What is the tool you used for analysis? Also please show an MA-plot and highlight the gene you are interested in. Your experiment could simply be underpower ...
written 1 day ago by
ATpoint ♦ 26k
1
vote
1
answer
68
views
1
answers
... What you want is a standard differential analysis. Look at tools such as `csaw` or `Diffbind` which are essentially wrappers for `DESeq2` and `edgeR`. The manuals cover all basic analysis steps. You input a count matrix and eventually get a list of regions with significant changes for H3K27me3 betwe ...
written 3 days ago by
ATpoint ♦ 26k
5
votes
2
answers
193
views
2
answers
... Well, not sure how to further help you from the bioinformatics side. You simply have no DEGs based on the current setup plus that potential batch effect. Probably have to go back to the lab and repeat the experiment. Was the gene that you checked by qPCR well-expressed or is it on the very left of t ...
written 3 days ago by
ATpoint ♦ 26k
Latest awards to ATpoint
Good Answer
1 day ago,
created an answer that was upvoted at least 5 times.
For C: Detect repeats problematic for PCR
Appreciated
1 day ago,
created a post with more than 5 votes.
For C: Detect repeats problematic for PCR
Teacher
1 day ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Teacher
5 days ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Scholar
11 days ago,
created an answer that has been accepted.
For A: Fasta extraction from bed file
Teacher
17 days ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Appreciated
19 days ago,
created a post with more than 5 votes.
For C: Detect repeats problematic for PCR
Teacher
19 days ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Teacher
19 days ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Teacher
19 days ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Teacher
21 days ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Teacher
25 days ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Teacher
27 days ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Scholar
27 days ago,
created an answer that has been accepted.
For A: Fasta extraction from bed file
Scholar
28 days ago,
created an answer that has been accepted.
For A: Fasta extraction from bed file
Teacher
29 days ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Commentator
29 days ago,
created a comment with at least 3 up-votes.
For C: How to run the Deseq2 tool without replicates.
Scholar
29 days ago,
created an answer that has been accepted.
For A: Fasta extraction from bed file
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: Fasta extraction from bed file
Appreciated
4 weeks ago,
created a post with more than 5 votes.
For C: Detect repeats problematic for PCR
Teacher
4 weeks ago,
created an answer with at least 3 up-votes.
For C: Detect repeats problematic for PCR
Scholar
4 weeks ago,
created an answer that has been accepted.
For A: Fasta extraction from bed file
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1301 users visited in the last hour