User: DVA

gravatar for DVA
DVA540
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 >
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Get Pseudotime Matrix in Monocole2?
... 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 ...
monocole2 written 11 months ago by DVA540
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5 follow
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Check Conservation of a Given Protein Domain
... 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 ...
blast written 18 months ago by DVA540 • updated 18 months ago by Bill Pearson860
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Comment: C: What happens when SNV caller looks at a SV (e.g. deletion) region?
... Thanks so much! I appreciate your help. ...
written 19 months ago by DVA540
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What happens when SNV caller looks at a SV (e.g. deletion) region?
... 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! ...
snv deletion written 19 months ago by DVA540 • updated 19 months ago by WouterDeCoster44k
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Differential Binding in Partek
... 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 ...
partek chip-seq atac-seq written 20 months ago by DVA540 • updated 20 months ago by kgosche30
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RNA Expression Pathway Database
... 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 ...
database written 21 months ago by DVA540 • updated 19 months ago by Biostar ♦♦ 20
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Comment: C: How to handle RNASeq reads that can map to both human and mouse ref (e.g. conser
... 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 DVA540
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How to handle RNASeq reads that can map to both human and mouse ref (e.g. conserved gene regions)?
... 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 ...
alignment hisat2 written 22 months ago by DVA540 • updated 22 months ago by JC11k
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Comment: C: CIGAR and sequence length are inconsistent after HISAT alignment
... Thank you for the conformation. I will update this post once I hear from them. ...
written 23 months ago by DVA540
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CIGAR and sequence length are inconsistent after HISAT alignment
... 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: ...
rnaseq hisat alignment written 23 months ago by DVA540 • updated 23 months ago by Devon Ryan96k

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

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