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2
votes
0
replies
715
views
Answer:
Answer: samtools index: failed to create index. ([E::hts_idx_push] NO_COOR reads not in
10 weeks ago by
svp
▴ 680
2
votes
0
replies
1.1k
views
Comment:
Comment: Calculation of TMB on gene level
6 months ago by
svp
▴ 680
2
votes
0
replies
1.1k
views
Comment:
Comment: Calculation of TMB on gene level
6 months ago by
svp
▴ 680
3
votes
1
reply
1.1k
views
Comment:
Comment: Calculation of TMB on gene level
6 months ago by
svp
▴ 680
4
votes
0
replies
379
views
Answer:
Answer: How to retrieve sample informations from given ID from Sequence Read Archives?
updated 4 months ago by
Ram
43k • written 6 months ago by
svp
▴ 680
0
votes
1
reply
1.5k
views
Comment:
Comment: conda error
20 months ago by
svp
▴ 680
0
votes
1
reply
1.5k
views
Answer:
Answer: conda error
20 months ago by
svp
▴ 680
5
votes
2
replies
817
views
Fastq: how can I check if they are from DNA or RNAseq data?
WES
Fastq
updated 20 months ago by
Antonio R. Franco
★ 5.1k • written 20 months ago by
svp
▴ 680
4
votes
0
replies
792
views
Answer:
A: Calling triovariants using varscan from a compressed mileup file ?
3.2 years ago by
svp
▴ 680
0
votes
0
replies
2.5k
views
Comment:
C: Is anybody experiencing problems downloading from the SRA?
3.2 years ago by
svp
▴ 680
2
votes
0
replies
2.8k
views
Comment:
C: How to call denovo and rare variants from a trios cohort?
3.2 years ago by
svp
▴ 680
4
votes
0
replies
1.1k
views
Comment:
C: CalculateGenotypePosteriors: A USER ERROR has occurred: Invalid argument ' '.
3.2 years ago by
svp
▴ 680
0
votes
0
replies
5.9k
views
Comment:
C: Combine two VCF files with GATK4
3.2 years ago by
svp
▴ 680
3
votes
0
replies
5.9k
views
Answer:
A: Combine two VCF files with GATK4
3.2 years ago by
svp
▴ 680
5
votes
0
replies
1.5k
views
Comment:
C: How do we deal with `MIXED` type variants in VQSR mode of Variant filtering ?
3.2 years ago by
svp
▴ 680
0
votes
0
replies
4.8k
views
Comment:
C: GATK4 VariantRecalibrator resource error
3.2 years ago by
svp
▴ 680
1
vote
0
replies
902
views
Comment:
C: How to call denovo variants from multiple trios cohort?
3.2 years ago by
svp
▴ 680
6
votes
0
replies
63k
views
Answer:
A: pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function
3.3 years ago by
svp
▴ 680
3
votes
0
replies
8.3k
views
Answer:
A: Generating heatmaps of pre-selected candidate genes after deseq2
3.3 years ago by
svp
▴ 680
1
vote
0
replies
1.5k
views
Comment:
C: Access metadata in GEO expression datasets
3.4 years ago by
svp
▴ 680
0
votes
0
replies
1.5k
views
Comment:
C: Access metadata in GEO expression datasets
3.4 years ago by
svp
▴ 680
1
vote
0
replies
1.0k
views
Comment:
C: Color code samples
3.5 years ago by
svp
▴ 680
0
votes
0
replies
908
views
Comment:
C: SNPs not filtered from a GATK vcf file
3.6 years ago by
svp
▴ 680
3
votes
0
replies
1.5k
views
Answer:
A: Web scraping in the KEGG db
3.6 years ago by
svp
▴ 680
2
votes
0
replies
5.2k
views
Answer:
A: RSEM Error - rsem-calculate-expression
3.6 years ago by
svp
▴ 680
2
votes
1
reply
1.2k
views
How to classify Tumor Mutation Burden into TMB high, medium and low groups ?
exome
tumor mutation burden
TMB
updated 3.6 years ago by
Karma
▴ 310 • written 3.6 years ago by
svp
▴ 680
2
votes
1
reply
1.3k
views
Does HaploypeCaller detects somatic mutations also?
HaplotypeCaller
Mutation
Exome
somatic
germline
updated 3.6 years ago by
WouterDeCoster
47k • written 3.6 years ago by
svp
▴ 680
6
votes
1
reply
2.1k
views
what is the difference between calling variants with and without interval list?
GATK
HaplotypeCaller
intervallist
updated 3.6 years ago by
Alewa
▴ 150 • written 3.6 years ago by
svp
▴ 680
0
votes
1
reply
606
views
How to interpret the values given in the BisoGenet output table ?
BisoGenet
protein interction nework
Cytoscape
updated 3.6 years ago by
scooter
▴ 620 • written 3.6 years ago by
svp
▴ 680
1
vote
0
replies
663
views
How to extract list of proteins delectable by immune histochemistry?
Immune Histochemistry
IHC
detection
cancer
3.7 years ago by
svp
▴ 680
1
vote
0
replies
933
views
Comment:
C: Calculation of Mentha Score
3.7 years ago by
svp
▴ 680
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
DESeq2
batcheffects
sva
combat
3.7 years ago by
svp
▴ 680
2
votes
0
replies
1.0k
views
Answer:
A: How to perform batch correction when we have only single condition?
3.7 years ago by
svp
▴ 680
0
votes
1
reply
4.2k
views
Comment:
C: Normalization of RNASeq read counts without conditions
3.7 years ago by
svp
▴ 680
6
votes
1
reply
1.7k
views
How can I call both somatic and germline variants from bam file?
exome
variant calling
somatic
germline
ngs
updated 3.7 years ago by
godth13teen
▴ 70 • written 3.7 years ago by
svp
▴ 680
0
votes
1
reply
37k
views
Answer:
A: Converting a VCF with SNPs and indels to BED format
3.7 years ago by
svp
▴ 680
0
votes
0
replies
1.1k
views
Comment:
C: Why snpEff annotates same region with different "effects" and why some effects a
3.8 years ago by
svp
▴ 680
0
votes
1
reply
1.1k
views
Comment:
C: Why snpEff annotates same region with different "effects" and why some effects a
3.8 years ago by
svp
▴ 680
0
votes
4
replies
1.1k
views
Why snpEff annotates same region with different "effects" and why some effects are given in combination? What is the criteria to filter this annotati…
snpEff
VEP
VariantAnnotation
Exome
VCF
3.8 years ago by
svp
▴ 680
2
votes
1
reply
716
views
How to convert genomic region of following type to vcf file?
VCF
Conversion
LiftOver
updated 3.8 years ago by
Pierre Lindenbaum
160k • written 3.8 years ago by
svp
▴ 680
5
votes
4
replies
7.8k
views
Why 'filterByExpr' does not eliminate low read counts from the expression data?
edgeR
RNA-Seq
DEGs
filterByExpr
updated 3.9 years ago by
Gordon Smyth
★ 6.9k • written 3.9 years ago by
svp
▴ 680
3
votes
0
replies
2.4k
views
Answer:
A: How do I run a .fastq single-end file in rsem-calculate-expression?
4.0 years ago by
svp
▴ 680
3
votes
1
reply
3.1k
views
What is the difference of output samtools depth and samtools view -c on location of bam file?
samtools
depth
count
bam
updated 4.0 years ago by
jkbonfield
★ 1.2k • written 4.1 years ago by
svp
▴ 680
1
vote
0
replies
1.1k
views
Answer:
A: How to get reference genome sequence given species name
4.1 years ago by
svp
▴ 680
0
votes
0
replies
3.5k
views
Answer:
A: depth calculation for targeted resequencing
4.1 years ago by
svp
▴ 680
0
votes
0
replies
12k
views
Comment:
C: Compute mean depth coverage for exome data with paired end, overlapping, feature
4.1 years ago by
svp
▴ 680
0
votes
1
reply
12k
views
Comment:
C: Compute mean depth coverage for exome data with paired end, overlapping, feature
4.1 years ago by
svp
▴ 680
0
votes
1
reply
12k
views
Comment:
C: Compute mean depth coverage for exome data with paired end, overlapping, feature
4.1 years ago by
svp
▴ 680
0
votes
1
reply
237k
views
Comment:
C: Tools To Calculate Average Coverage For A Bam File?
4.1 years ago by
svp
▴ 680
0
votes
1
reply
785
views
How to extract coverage of custom target regions (bed file) from a bam file?
coverage
bedtools
4.1 years ago by
svp
▴ 680
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