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User: DVA

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DVA • 530
Reputation:
530
Status:
Trusted
Location:
United States
Last seen:
3 months ago
Joined:
4 years, 10 months ago
Email:
s***********@gmail.com

Posts by DVA

<prev • 154 results • page 1 of 16 • next >
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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 4 months ago by DVA • 530 • updated 4 months ago by Bill Pearson • 860
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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 4 months ago by DVA • 530
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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 4 months ago by DVA • 530 • updated 4 months ago by WouterDeCoster ♦ 40k
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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 5 months ago by DVA • 530 • updated 5 months ago by kgosche • 0
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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 7 months ago by DVA • 530 • updated 5 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 7 months ago by DVA • 530
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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 7 months ago by DVA • 530 • updated 7 months ago by JC ♦ 8.0k
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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 8 months ago by DVA • 530
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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 8 months ago by DVA • 530 • updated 8 months ago by Devon Ryan ♦ 91k
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Comment: C: Count 0, 5, 20 covered sites in bam
... Thanks for the help! Appreciate it. ...
written 10 months ago by DVA • 530

Latest awards to DVA

Popular Question 3 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Illumina's HiSeq strange Phred quality score
Popular Question 4 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 4 months ago, created a question with more than 1,000 views. For Output all allele counts at each position using bcftools
Popular Question 5 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 7 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 7 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 9 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 9 months ago, created a question with more than 1,000 views. For Output all allele counts at each position using bcftools
Popular Question 10 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Voter 16 months ago, voted more than 100 times.
Popular Question 18 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 18 months ago, created a question with more than 1,000 views. For Output all allele counts at each position using bcftools
Popular Question 18 months ago, created a question with more than 1,000 views. For Manually edit the flags in a sam file
Popular Question 19 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Centurion 19 months ago, created 100 posts.
Popular Question 23 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Appreciated 23 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Popular Question 23 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 24 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 2.1 years ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Student 2.3 years ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 2.4 years ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Appreciated 2.5 years ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Good Question 2.5 years ago, asked a question that was upvoted at least 5 times. For Develop an R package for CRAN vs BioConductor
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