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0
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2
replies
3.0k
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Comment: C: Automatically feeding a good mate inner distance to TopHat2
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
0
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0
replies
2.7k
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Comment: C: Cutadapt paired end reads with 1 adapter list fasta
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
0
replies
2.9k
views
Comment: C: CGHub/TCGA RNA-Seq data trimming adapters
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
1
vote
1
reply
2.7k
views
Answer: A: bcftools "The argument to -g not recognised"
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
15k
views
Comment: C: Where to get list of all Illumina adapters
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
1
vote
1
reply
2.4k
views
Comment: C: Using ref.fa (with random contig) on bam file aligned without random contigs
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
2.9k
views
Comment: C: Request for karyotypically sorted Ensembl reference fasta and its dbSNP vcf for
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
0
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1
reply
3.7k
views
Comment: C: Automating pre-alignment (and post-alignment) quality control
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
0
replies
7.4k
views
Comment: C: Change chromosome notation to match a new reference
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
3.7k
views
Comment: C: Automating pre-alignment (and post-alignment) quality control
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
2.8k
views
Comment: C: Mixed opinions on somatic variant calling method
updated 4.3 years ago by 43k • written 8.2 years ago by ▴ 390
13
votes
9
replies
3.0k
views
Automatically feeding a good mate inner distance to TopHat2
RNA-Seq TopHat PE
updated 24 months ago by 43k • written 8.2 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 2.8 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
0
replies
3.5k
views
Comment: C: NCBI dbSNP compatibility w/ Ensembl whole genome
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
0
replies
3.5k
views
Comment: C: NCBI dbSNP compatibility w/ Ensembl whole genome
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
0
replies
3.0k
views
Comment: C: Bam file doesn't show on IGV and pileup VCF has only header
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
3.0k
views
Comment: C: Bam file doesn't show on IGV and pileup VCF has only header
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
0
replies
3.0k
views
Comment: C: Bam file doesn't show on IGV and pileup VCF has only header
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
3.0k
views
Comment: C: Bam file doesn't show on IGV and pileup VCF has only header
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
3.0k
views
Comment: C: Bam file doesn't show on IGV and pileup VCF has only header
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
3.0k
views
Comment: C: Bam file doesn't show on IGV and pileup VCF has only header
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
0
replies
2.1k
views
Comment: C: [GATK] Weird error using Picard SortVcf on COSMIC file
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
1.9k
views
Comment: C: No somatic mutation in tumor sample
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
1
reply
1.9k
views
Answer: A: No somatic mutation in tumor sample
updated 5.6 years ago by 43k • written 8.2 years ago by ▴ 390
0
votes
0
replies
1.9k
views
Comment: C: No somatic mutation in tumor sample
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 7.8 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 7.9 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 7.9 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 3.0 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 8.0 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
5.8k
views
Comment: C: Bowtie memory warning
8.0 years ago by umn_bist ▴ 390
0
votes
0
replies
2.5k
views
[mutect2] vcf 4.1 instead of vcf 4.2?
RNA-Seq vcf mutect2
8.0 years ago by umn_bist ▴ 390
5
votes
11
replies
3.8k
views
Salmon/Sailfish for repeat element quantification?
RNA-Seq DE
updated 8.0 years ago by ★ 3.0k • written 8.0 years ago by ▴ 390
0
votes
1
reply
3.8k
views
Comment: C: Salmon/Sailfish for repeat element quantification?
8.0 years ago by umn_bist ▴ 390
4
votes
0
replies
2.2k
views
Broad Institute TCGA MAF procedure
RNA-Seq SNV MAF TCGA
8.0 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
0
votes
1
reply
5.0k
views
Comment: C: GATK MuTect2 duplication filter
8.1 years ago by umn_bist ▴ 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
124 results • Page 1 of 3
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