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13
votes
9
replies
3.1k
views
Automatically feeding a good mate inner distance to TopHat2
RNA-Seq TopHat PE
updated 2.0 years ago by 43k • written 8.3 years ago by ▴ 390
1
vote
1
reply
2.0k
views
TCGA Broad Institute curated variants
RNA-Seq TCGA Broad Institute SNV
updated 5.1 years ago by 20 • written 8.0 years ago by ▴ 390
5
votes
5
replies
3.5k
views
NCBI dbSNP compatibility w/ Ensembl whole genome
GATK Ensembl NCBI
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
5
votes
7
replies
3.6k
views
[ERROR] Malformed VCF: empty alleles are not permitted in VCF records
VCF GATK RNA-Seq
updated 2.9 years ago by • 0 • written 8.2 years ago by ▴ 390
5
votes
12
replies
3.0k
views
Bam file doesn't show on IGV and pileup VCF has only header
RNA-Seq
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
2
replies
11k
views
[STAR] 255 Mapping Quality
RNA-Seq MuTect2 STAR
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
3
votes
2
replies
2.1k
views
[GATK] Weird error using Picard SortVcf on COSMIC file
GATK RNA-Seq MuTect2 picard
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
3
replies
1.4k
views
Frequency of codon mutation in cancer
IARC TCGA
updated 7.9 years ago by 13k • written 8.0 years ago by ▴ 390
7
votes
9
replies
5.6k
views
STAR add RG
RNA-Seq STAR RGID GATK
updated 8.0 years ago by 20 • written 8.2 years ago by ▴ 390
0
votes
0
replies
2.5k
views
MuTect2 - vcf 4.1 instead of vcf 4.2
RNA-Seq GATK MuTect2 VCF
updated 8.0 years ago by 20 • written 8.0 years ago by ▴ 390
1
vote
3
replies
6.3k
views
Is there a way to reformat vcf 4.2 down to 4.1?
variant calling snpSift snpEff
updated 3.1 years ago by • 0 • written 8.0 years ago by ▴ 390
4
votes
2
replies
2.1k
views
retrotransposon RNAseq quantification and ChIPseq peak calling tools/guides?
RNA-Seq ChIP-Seq retrotransposon
updated 8.0 years ago by 100k • written 8.1 years ago by ▴ 390
2
votes
1
reply
5.3k
views
MuTect2's variants missing QUAL score
RNA-Seq MuTect2 VCF 4.2 GATK
updated 8.0 years ago by 100k • written 8.1 years ago by ▴ 390
3
votes
7
replies
5.8k
views
Bowtie memory warning
bowtie
updated 8.0 years ago by 100k • written 8.0 years ago by ▴ 390
8
votes
14
replies
2.6k
views
8 follow
Any experience using SomaticSeq for RNAseq SNV?
RNAseq
updated 2.5 years ago by ▴ 140 • written 8.0 years ago by ▴ 390
0
votes
0
replies
2.5k
views
[mutect2] vcf 4.1 instead of vcf 4.2?
RNA-Seq vcf mutect2
8.1 years ago by umn_bist ▴ 390
5
votes
11
replies
3.8k
views
Salmon/Sailfish for repeat element quantification?
RNA-Seq DE
updated 8.1 years ago by ★ 3.0k • written 8.1 years ago by ▴ 390
4
votes
0
replies
2.2k
views
Broad Institute TCGA MAF procedure
RNA-Seq SNV MAF TCGA
8.1 years ago by umn_bist ▴ 390
2
votes
2
replies
2.3k
views
Fasta output from bedtools GetFastaBed
ChIP-Seq BWA
updated 8.1 years ago by ★ 2.9k • written 8.1 years ago by ▴ 390
0
votes
1
reply
2.1k
views
[TCGA] Statistical analysis of somatic variant calling
RNA-Seq TCGA
updated 8.1 years ago by ★ 4.7k • written 8.1 years ago by ▴ 390
2
votes
2
replies
1.6k
views
Searching for primers (and its rev compl.) in PACMAN
plasmid
updated 8.1 years ago by 3.2k • written 8.1 years ago by ▴ 390
1
vote
3
replies
5.0k
views
GATK MuTect2 duplication filter
RNA-Seq GATK
updated 8.1 years ago by 7.3k • written 8.1 years ago by ▴ 390
0
votes
1
reply
2.4k
views
[cBioPortal] [GATK] [TCGA] Somatic variant calling error
RNA-Seq GATK cBioPortal TCGA
8.1 years ago by umn_bist ▴ 390
3
votes
3
replies
2.3k
views
Managing large data sets
TCGA RNAseq
updated 8.1 years ago by ★ 4.9k • written 8.1 years ago by ▴ 390
0
votes
0
replies
1.6k
views
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
votes
2
replies
1.9k
views
cBioPortal 'Mutations' tab
cBioPortal TCGA
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 8.2 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
votes
1
reply
2.0k
views
(Error) bedtools fastafrombed and STAR aligner
RNA-Seq STAR bedtools
8.2 years ago by umn_bist ▴ 390
4
votes
7
replies
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
votes
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
15
votes
7
replies
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
votes
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
votes
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
2
votes
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
4
votes
12
replies
8.4k
views
UCSC hg19 gtf (genePredToGtf OS incompatibility)
RNA-Seq genome
8.2 years ago by umn_bist ▴ 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
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
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
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
3
votes
2
replies
2.7k
views
Cutadapt paired end reads with 1 adapter list fasta
RNA-Seq Illumina cutadapt
updated 21 months ago by 43k • written 8.3 years ago by ▴ 390
3
votes
2
replies
3.0k
views
CGHub/TCGA RNA-Seq data trimming adapters
FastQC Illumina cutadapt SolexaQA-plus-plus RNA-Seq
updated 21 months ago by 43k • written 8.3 years ago by ▴ 390
2
votes
0
replies
5.0k
views
Good filtering practices for VCF (Bcftools 1.3)
RNA-Seq VCF bcftools samtools
updated 21 months ago by 43k • written 8.3 years ago by ▴ 390
7
votes
6
replies
15k
views
Where to get list of all Illumina adapters
RNA-Seq Illumina cutadapt adapters
updated 21 months ago by 43k • written 8.3 years ago by ▴ 390
59 results • Page 1 of 2
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