User: DVA
DVA • 480
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Posts by DVA
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... Thank you for the conformation. I will update this post once I hear from them. ...
written 13 days ago by
DVA • 480
0
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... 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 15 days ago by
DVA • 480
• updated
15 days ago by
Devon Ryan ♦ 86k
1
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2
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... Thanks for the help! Appreciate it. ...
written 8 weeks ago by
DVA • 480
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... Thank you for the comment @genomax, I am looking at individual base level. ...
written 8 weeks ago by
DVA • 480
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... 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. ...
written 8 weeks ago by
DVA • 480
• updated
8 weeks ago by
Pierre Lindenbaum ♦ 114k
1
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210
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... 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 ...
written 4 months ago by
DVA • 480
0
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... Thanks so much for the information! ...
written 5 months ago by
DVA • 480
3
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1
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... 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 ...
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... 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 ...
written 5 months ago by
DVA • 480
• updated
5 months ago by
c.chakraborty • 110
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7 weeks ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
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7 weeks ago,
created a question with more than 1,000 views.
For Output all allele counts at each position using bcftools
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10 weeks ago,
created a question with more than 1,000 views.
For Non-cancer somatic mutation calling
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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,
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For Manually edit the flags in a sam file
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11 months ago,
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For Non-cancer somatic mutation calling
Centurion
11 months ago,
created 100 posts.
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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
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15 months ago,
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For Non-cancer somatic mutation calling
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16 months ago,
created a question with more than 1,000 views.
For Remove both pair end reads with low mapping quality using Samtools
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17 months ago,
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For Remove both pair end reads with low mapping quality using Samtools
Student
20 months ago,
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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,
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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,
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For Non-cancer somatic mutation calling
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24 months ago,
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For Identify point mutations from each read in sam files
Student
2.0 years ago,
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For Non-cancer somatic mutation calling
Student
2.5 years ago,
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For Non-cancer somatic mutation calling
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For A: Can't locate dbSNP 131 anymore?
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For A: Illumina's HiSeq strange Phred quality score
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2.7 years ago,
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For A: Can't locate dbSNP 131 anymore?
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