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TCGA: Bash assigning a tumor to its match normal
RNA-Seq TCGA MuTect2
updated 21 months ago by 43k • written 8.2 years ago by ▴ 390
0
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0
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1.9k
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Comment: C: cBioPortal 'Mutations' tab
8.1 years ago by umn_bist ▴ 390
0
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2
replies
1.9k
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cBioPortal 'Mutations' tab
cBioPortal TCGA
8.1 years ago by umn_bist ▴ 390
0
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1
reply
4.3k
views
Comment: C: BBDuk trimming concern: large discarded, too aggressive (?)
8.1 years ago by umn_bist ▴ 390
0
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1
reply
4.3k
views
Comment: C: BBDuk trimming concern: large discarded, too aggressive (?)
8.1 years ago by umn_bist ▴ 390
0
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0
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4.3k
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Comment: C: BBDuk trimming concern: large discarded, too aggressive (?)
8.1 years ago by umn_bist ▴ 390
3
votes
7
replies
4.3k
views
BBDuk trimming concern: large discarded, too aggressive (?)
BBDuk RNA-Seq
8.1 years ago by umn_bist ▴ 390
1
vote
1
reply
1.5k
views
Associativity between 2 cancer types
statistics SNP RNA-Seq
updated 8.1 years ago by 20 • written 8.2 years ago by ▴ 390
6
votes
8
replies
4.4k
views
How to build a custom reference genome (from a BED file)
RNA-Seq
updated 8.2 years ago by ▴ 380 • written 8.2 years ago by ▴ 390
0
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1
reply
2.0k
views
(Error) bedtools fastafrombed and STAR aligner
RNA-Seq STAR bedtools
8.2 years ago by umn_bist ▴ 390
0
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2
replies
4.4k
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Comment: C: How to build a custom reference genome (from a BED file)
8.2 years ago by umn_bist ▴ 390
0
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0
replies
1.9k
views
Comment: C: Faster alternative to Prinseq PE trimming polyN
8.2 years ago by umn_bist ▴ 390
0
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1
reply
1.9k
views
Comment: C: Faster alternative to Prinseq PE trimming polyN
8.2 years ago by umn_bist ▴ 390
0
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1
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1.9k
views
Comment: C: Faster alternative to Prinseq PE trimming polyN
8.2 years ago by umn_bist ▴ 390
4
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7
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1.9k
views
Faster alternative to Prinseq PE trimming polyN
RNA-Seq prinseq BBDuk
updated 8.2 years ago by 43k • written 8.2 years ago by ▴ 390
0
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1
reply
2.3k
views
STAR aligner with singletons and short reads
RNA-Seq STAR
updated 21 months ago by 43k • written 8.2 years ago by ▴ 390
25
votes
7
replies
5.6k
views
7 follow
Why is normal blood used for matched tumor (instead of adjacent norm tissue)?
RNA-Seq
updated 8.2 years ago by 22k • written 8.2 years ago by ▴ 390
0
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1
reply
5.6k
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Comment: C: Why is normal blood used for matched tumor (instead of adjacent norm tissue)?
8.2 years ago by umn_bist ▴ 390
0
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0
replies
10.0k
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Comment: C: FastQC: 'Per base sequence content' for RNA-Seq
8.2 years ago by umn_bist ▴ 390
15
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7
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10.0k
views
FastQC: 'Per base sequence content' for RNA-Seq
RNA-Seq
updated 8.2 years ago by 142k • written 8.2 years ago by ▴ 390
6
votes
2
replies
2.8k
views
TCGA tumor/normal RNA-seq somatic mutation calling
RNA-Seq TCGA
updated 8.2 years ago by ▴ 620 • written 8.2 years ago by ▴ 390
0
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6
replies
1.9k
views
No somatic mutation in tumor sample
RNA-Seq STAR picard cutadapt prinseq
8.2 years ago by umn_bist ▴ 390
0
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1
reply
3.6k
views
Comment: C: [ERROR] Malformed VCF: empty alleles are not permitted in VCF records
8.2 years ago by umn_bist ▴ 390
0
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1
reply
3.5k
views
Comment: C: NCBI dbSNP compatibility w/ Ensembl whole genome
8.2 years ago by umn_bist ▴ 390
0
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0
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2.1k
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Comment: C: RNA-seq expression profiling
8.2 years ago by umn_bist ▴ 390
0
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2
replies
2.1k
views
RNA-seq expression profiling
RNA-Seq TopHat2 STAR
updated 8.2 years ago by 13k • written 8.2 years ago by ▴ 390
0
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1
reply
2.8k
views
Comment: C: How to generate a mask gtf for use with cufflinks
8.2 years ago by umn_bist ▴ 390
0
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1
reply
1.9k
views
Comment: C: Conceptual question regarding retrotransposon (RNA-seq) analysis
8.2 years ago by umn_bist ▴ 390
2
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3
replies
1.9k
views
Conceptual question regarding retrotransposon (RNA-seq) analysis
rna-seq
updated 21 months ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
2.6k
views
Confusing header after mapping w/ STAR using Ensembl refgenome
RNA-Seq STAR samtools Ensembl GrCh38.p5
updated 21 months ago by 43k • written 8.2 years ago by ▴ 390
0
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1
reply
8.3k
views
Comment: C: UCSC hg19 gtf (genePredToGtf OS incompatibility)
8.2 years ago by umn_bist ▴ 390
0
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0
replies
8.3k
views
Comment: C: UCSC hg19 gtf (genePredToGtf OS incompatibility)
8.2 years ago by umn_bist ▴ 390
0
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1
reply
8.3k
views
Comment: C: UCSC hg19 gtf (genePredToGtf OS incompatibility)
8.2 years ago by umn_bist ▴ 390
0
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0
replies
8.3k
views
Answer: A: UCSC hg19 gtf (genePredToGtf OS incompatibility)
8.2 years ago by umn_bist ▴ 390
4
votes
12
replies
8.3k
views
UCSC hg19 gtf (genePredToGtf OS incompatibility)
RNA-Seq genome
8.2 years ago by umn_bist ▴ 390
0
votes
1
reply
1.6k
views
Comment: Comment: Trouble using if string in column 3 of .csv exist, then statement
updated 21 months ago by 43k • written 8.2 years ago by ▴ 390
0
votes
3
replies
1.6k
views
Trouble using if string in column 3 of .csv exist, then statement
TCGA bash
updated 21 months ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
2.3k
views
[GATK] [MuTect2] [RNA-Seq] Adding read group ahead of annotations
RNA-Seq Picard GATK MuTect2
updated 21 months ago by 43k • written 8.3 years ago by ▴ 390
0
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0
replies
5.6k
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Comment: C: STAR add RG
8.2 years ago by umn_bist ▴ 390
0
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1
reply
5.6k
views
Comment: C: STAR add RG
8.2 years ago by umn_bist ▴ 390
0
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0
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5.6k
views
Answer: A: STAR add RG
8.2 years ago by umn_bist ▴ 390
0
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2
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5.6k
views
Comment: C: STAR add RG
8.2 years ago by umn_bist ▴ 390
2
votes
4
replies
3.4k
views
RNA-seq dedupe PCR contamination before or after mapping
RNA-Seq
updated 8.2 years ago by 8.7k • written 8.2 years ago by ▴ 390
0
votes
1
reply
3.4k
views
Comment: C: RNA-seq dedupe PCR contamination before or after mapping
8.2 years ago by umn_bist ▴ 390
0
votes
0
replies
1.6k
views
Request to validate my RNAseq workflow
RNA-Seq NGS
8.2 years ago by umn_bist ▴ 390
0
votes
1
reply
1.9k
views
Pipeline for >100 RNA-Seq PE samples
RNA-Seq
updated 21 months ago by 43k • written 8.2 years ago by ▴ 390
0
votes
0
replies
1.9k
views
Comment: C: Pipeline for >100 RNA-Seq PE samples
8.2 years ago by umn_bist ▴ 390
0
votes
1
reply
4.2k
views
Comment: C: cutadapt: forward and reverse adapter sequence options
8.2 years ago by umn_bist ▴ 390
0
votes
3
replies
4.2k
views
cutadapt: forward and reverse adapter sequence options
RNA-Seq cutadapt
updated 21 months ago by 43k • written 8.2 years ago by ▴ 390
0
votes
0
replies
3.1k
views
Comment: C: Automatically feeding a good mate inner distance to TopHat2
8.3 years ago by umn_bist ▴ 390
124 results • Page 2 of 3
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