User: DVA

gravatar for DVA
DVA480
Reputation:
480
Status:
Trusted
Location:
United States
Last seen:
1 day, 14 hours ago
Joined:
4 years, 2 months ago
Email:
s***********@gmail.com

Posts by DVA

<prev • 147 results • page 1 of 15 • next >
0
votes
1
answer
99
views
1
answers
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 13 days ago by DVA480
0
votes
1
answer
99
views
1
answer
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 15 days ago by DVA480 • updated 15 days ago by Devon Ryan86k
1
vote
2
answers
150
views
2
answers
Comment: C: Count 0, 5, 20 covered sites in bam
... Thanks for the help! Appreciate it. ...
written 8 weeks ago by DVA480
0
votes
2
answers
150
views
2
answers
Comment: C: Count 0, 5, 20 covered sites in bam
... Thank you very much! ...
written 8 weeks ago by DVA480
0
votes
2
answers
150
views
2
answers
Comment: C: Count 0, 5, 20 covered sites in bam
... Thank you for the comment @genomax, I am looking at individual base level. ...
written 8 weeks ago by DVA480
4
votes
2
answers
150
views
2
answers
Count 0, 5, 20 covered sites in bam
... Hello, I wonder how to use a bam file to learn how many sites are not covered at all, how many are covered >=5 times and 20 times. We got such stats from our sequencing company, but want to see we can do it ourselves as well. Thank you very much. ...
wgs bam written 8 weeks ago by DVA480 • updated 8 weeks ago by Pierre Lindenbaum114k
1
vote
0
answers
210
views
0
answers
Extract the overlap of well-covered regions across multiple samples
... I am looking at somatic mutations across multiple samples, but the samples are not covered equally in many regions. Since we care about comparing the mutation counts between these samples, I would need to consider the uneven coverage -- e.g. sample A has 5X coverage at position 1, while sample B has ...
wgs coverage written 4 months ago by DVA480
0
votes
1
answer
227
views
1
answers
Comment: C: Pathway enrichment with differential expression p-values
... Thanks so much for the information! ...
written 5 months ago by DVA480
3
votes
1
answer
227
views
1
answer
Pathway enrichment with differential expression p-values
... Hello All, I have a large set of genes with differential expression p-values (from DEseq2) and directional (up or down-regulated) information. I was wondering if anyone knew of a pathway enrichment analysis program that could make use of all of this information rather than just the gene list? Sorry ...
gene enrichment written 5 months ago by DVA480 • updated 5 months ago by b.nota5.3k
1
vote
1
answer
289
views
1
answer
GSEA Phenotype Table Input
... Hello All, I am trying use GSEA for gene enrichment analysis, and I was wondering about the phenotype labels. Is there a way to test for the difference between two phenotypes while controlling for other phenotypes in a different category? For example, if I wanted to compare 5 cancer samples to 5 ...
gsea written 5 months ago by DVA480 • updated 5 months ago by c.chakraborty110

Latest awards to DVA

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Output all allele counts at each position using bcftools
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Voter 8 months ago, voted more than 100 times.
Popular Question 10 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 10 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 Manually edit the flags in a sam file
Popular Question 11 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Centurion 11 months ago, created 100 posts.
Popular Question 15 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Appreciated 15 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Popular Question 15 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 16 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 17 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Student 20 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 20 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Appreciated 22 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Good Question 22 months ago, asked a question that was upvoted at least 5 times. For Develop an R package for CRAN vs BioConductor
Student 22 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 24 months ago, created a question with more than 1,000 views. For Identify point mutations from each read in sam files
Student 2.0 years ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Student 2.5 years ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Scholar 2.5 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?
Teacher 2.5 years ago, created an answer with at least 3 up-votes. For A: Illumina's HiSeq strange Phred quality score
Scholar 2.7 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1844 users visited in the last hour