User: DVA
DVA • 540
- Reputation:
- 540
- Status:
- Trusted
- Location:
- United States
- Last seen:
- 11 months, 3 weeks ago
- Joined:
- 6 years ago
- Email:
- s***********@gmail.com
Posts by DVA
<prev
• 155 results •
page 1 of 16 •
next >
0
votes
0
answers
354
views
0
answers
... I have been using Monocole2 to study the progression of cells into a disease state and have had good results clustering the cells, identifying deferentially expressed genes, and plotting a pseudotime continuum.
However, I would also like to identify genes that are critical to the initial transitio ...
written 11 months ago by
DVA • 540
2
votes
1
answer
378
views
5 follow
1
answer
... Hello,
I am interested in a small domain of a well studied and well defined protein (Huntingtin), and would like to see how conserved this domain is across species. In particular, I would like to address two questions in a scientific (publishable) way:
How well conserved across species is this do ...
written 18 months ago by
DVA • 540
• updated
18 months ago by
Bill Pearson • 860
0
votes
1
answer
381
views
1
answers
... Thanks so much! I appreciate your help. ...
written 19 months ago by
DVA • 540
4
votes
1
answer
381
views
1
answer
... Hello,
I hope this question is not too silly. What would happen to SNVs callers such as GATK, if a region has some kind of structure variations? Would the caller be able to tell?
Thank you! ...
written 19 months ago by
DVA • 540
• updated
19 months ago by
WouterDeCoster ♦ 44k
0
votes
1
answer
500
views
1
answer
... Hello,
Does anyone have a protocol or recommended pipeline for doing differential peak/binding analysis in Partek. I want to compare ATAC-seq results from two different conditions, but a ChIP-seq based pipeline would also be useful.
Diffbind and csaw seem good but these are not available in Parte ...
0
votes
0
answers
449
views
0
answers
... Could you please recommend me a database where I can get gene expression pathway data? Essentially, this database should have information along the lines of "expression of X causes an increase/decrease in the expression of Y".
I am studying RNA-seq data and information about "protein X binds prote ...
0
votes
1
answer
430
views
1
answers
... Hi @JC, thanks a lot for the reply! This is an interesting point - for the human case, it falls at the end with only one of the isoforms it seems like. I guess to use this design, that would require a very thorough annotation. ...
written 22 months ago by
DVA • 540
1
vote
1
answer
430
views
1
answer
... Hello,
I have a few 3' RNA sequencing data sets that have mixed human and mouse samples. As I am trying to split these reads apart, during the alignment (transcript region only) step, I noticed that there are about 3-5% of reads that can be mapped to both references - with VERY similar map-able bas ...
0
votes
1
answer
759
views
1
answers
... Thank you for the conformation. I will update this post once I hear from them. ...
written 23 months ago by
DVA • 540
0
votes
1
answer
759
views
1
answer
... Hello,
I am trying to understand an error when running "samtools view":
Line 6040, sequence length 67 vs 76 from CIGAR
Parse error at line 6040: CIGAR and sequence length are inconsistent
I went back to check line 6040 from sam file (generated by HISAT2):
NR500449:117:H7WMXX:2:11101: ...
written 23 months ago by
DVA • 540
• updated
23 months ago by
Devon Ryan ♦ 96k
Latest awards to DVA
Great Question
17 months ago,
created a question with more than 5,000 views.
For How do people know to use at least 30X coverage in WGS?
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Output all allele counts at each position using bcftools
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Extract genotype from hg19
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Can't locate dbSNP 131 anymore?
Popular Question
17 months ago,
created a question with more than 1,000 views.
For VCFtools: how does --diff option consider genotypes
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Manually edit the flags in a sam file
Popular Question
17 months ago,
created a question with more than 1,000 views.
For Remove both pair end reads with low mapping quality using Samtools
Popular Question
18 months ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Teacher
18 months ago,
created an answer with at least 3 up-votes.
For A: Illumina's HiSeq strange Phred quality score
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Popular Question
19 months ago,
created a question with more than 1,000 views.
For Output all allele counts at each position using bcftools
Popular Question
20 months ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Popular Question
21 months ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Popular Question
22 months ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Popular Question
2.0 years ago,
created a question with more than 1,000 views.
For Output all allele counts at each position using bcftools
Popular Question
2.1 years ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Voter
2.6 years ago,
voted more than 100 times.
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Output all allele counts at each position using bcftools
Popular Question
2.7 years ago,
created a question with more than 1,000 views.
For Manually edit the flags in a sam file
Popular Question
2.8 years ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Centurion
2.8 years ago,
created 100 posts.
Popular Question
3.1 years ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
Appreciated
3.1 years ago,
created a post with more than 5 votes.
For Develop an R package for CRAN vs BioConductor
Use of this site constitutes acceptance of our User
Agreement
and Privacy
Policy.
Powered by Biostar
version 2.3.0
Traffic: 1494 users visited in the last hour