User: DVA

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DVA490
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490
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Trusted
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United States
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Joined:
4 years, 4 months ago
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Posts by DVA

<prev • 150 results • page 1 of 15 • next >
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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 5 weeks ago by DVA490 • updated 4 weeks 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 8 weeks ago by DVA490
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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 8 weeks ago by DVA490 • updated 8 weeks ago by JC7.1k
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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 10 weeks ago by DVA490
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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 11 weeks ago by DVA490 • updated 11 weeks ago by Devon Ryan87k
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Comment: C: Count 0, 5, 20 covered sites in bam
... Thanks for the help! Appreciate it. ...
written 4 months ago by DVA490
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Comment: C: Count 0, 5, 20 covered sites in bam
... Thank you very much! ...
written 4 months ago by DVA490
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Comment: C: Count 0, 5, 20 covered sites in bam
... Thank you for the comment @genomax, I am looking at individual base level. ...
written 4 months ago by DVA490
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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 4 months ago by DVA490 • updated 4 months ago by Pierre Lindenbaum116k
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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 6 months ago by DVA490

Latest awards to DVA

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 3 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 3 months ago, created a question with more than 1,000 views. For Output all allele counts at each position using bcftools
Popular Question 4 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Voter 10 months ago, voted more than 100 times.
Popular Question 12 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Popular Question 12 months ago, created a question with more than 1,000 views. For Output all allele counts at each position using bcftools
Popular Question 12 months ago, created a question with more than 1,000 views. For Manually edit the flags in a sam file
Popular Question 13 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Centurion 13 months ago, created 100 posts.
Popular Question 17 months ago, created a question with more than 1,000 views. For Non-cancer somatic mutation calling
Appreciated 17 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Popular Question 17 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 Remove both pair end reads with low mapping quality using Samtools
Popular Question 19 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Student 22 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 23 months ago, created a question with more than 1,000 views. For Remove both pair end reads with low mapping quality using Samtools
Appreciated 24 months ago, created a post with more than 5 votes. For Develop an R package for CRAN vs BioConductor
Good Question 24 months ago, asked a question that was upvoted at least 5 times. For Develop an R package for CRAN vs BioConductor
Student 24 months ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Identify point mutations from each read in sam files
Student 2.2 years ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Student 2.7 years ago, asked a question with at least 3 up-votes. For Non-cancer somatic mutation calling
Scholar 2.7 years ago, created an answer that has been accepted. For A: Can't locate dbSNP 131 anymore?

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