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3
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Answer: Answer: samtools index: failed to create index. ([E::hts_idx_push] NO_COOR reads not in
17 months ago by svp ▴ 690
2
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2.0k
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Comment: Comment: Calculation of TMB on gene level
21 months ago by svp ▴ 690
2
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2.0k
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Comment: Comment: Calculation of TMB on gene level
21 months ago by svp ▴ 690
3
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1
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2.0k
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Comment: Comment: Calculation of TMB on gene level
21 months ago by svp ▴ 690
4
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721
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Answer: Answer: How to retrieve sample informations from given ID from Sequence Read Archives?
updated 19 months ago by 45k • written 21 months ago by ▴ 690
0
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1
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2.3k
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Comment: Comment: conda error
2.9 years ago by svp ▴ 690
0
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1
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2.3k
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Answer: Answer: conda error
2.9 years ago by svp ▴ 690
5
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2
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1.4k
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Fastq: how can I check if they are from DNA or RNAseq data?
WES Fastq
updated 2.9 years ago by ★ 5.2k • written 2.9 years ago by ▴ 690
4
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0
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1.1k
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Answer: A: Calling triovariants using varscan from a compressed mileup file ?
4.4 years ago by svp ▴ 690
0
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0
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3.4k
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Comment: C: Is anybody experiencing problems downloading from the SRA?
4.4 years ago by svp ▴ 690
2
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3.9k
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Comment: C: How to call denovo and rare variants from a trios cohort?
4.4 years ago by svp ▴ 690
4
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0
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1.4k
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Comment: C: CalculateGenotypePosteriors: A USER ERROR has occurred: Invalid argument ' '.
4.4 years ago by svp ▴ 690
0
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0
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8.6k
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Comment: C: Combine two VCF files with GATK4
4.4 years ago by svp ▴ 690
3
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8.6k
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Answer: A: Combine two VCF files with GATK4
4.4 years ago by svp ▴ 690
5
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0
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2.0k
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Comment: C: How do we deal with `MIXED` type variants in VQSR mode of Variant filtering ?
4.4 years ago by svp ▴ 690
0
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0
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5.9k
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Comment: C: GATK4 VariantRecalibrator resource error
4.4 years ago by svp ▴ 690
1
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0
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1.3k
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Comment: C: How to call denovo variants from multiple trios cohort?
4.4 years ago by svp ▴ 690
6
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0
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80k
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Answer: A: pheatmap: Error in hclust(d, method = method) : NA/NaN/Inf in foreign function
4.6 years ago by svp ▴ 690
3
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0
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9.7k
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Answer: A: Generating heatmaps of pre-selected candidate genes after deseq2
4.6 years ago by svp ▴ 690
1
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0
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2.1k
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Comment: C: Access metadata in GEO expression datasets
4.6 years ago by svp ▴ 690
0
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0
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2.1k
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Comment: C: Access metadata in GEO expression datasets
4.7 years ago by svp ▴ 690
1
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0
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1.3k
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Comment: C: Color code samples
4.7 years ago by svp ▴ 690
0
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0
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1.3k
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Comment: C: SNPs not filtered from a GATK vcf file
4.8 years ago by svp ▴ 690
3
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2.0k
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Answer: A: Web scraping in the KEGG db
4.8 years ago by svp ▴ 690
2
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0
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6.3k
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Answer: A: RSEM Error - rsem-calculate-expression
4.8 years ago by svp ▴ 690
2
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1
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1.5k
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How to classify Tumor Mutation Burden into TMB high, medium and low groups ?
exome tumor mutation burden TMB
updated 4.8 years ago by ▴ 310 • written 4.8 years ago by ▴ 690
2
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1
reply
1.7k
views
Does HaploypeCaller detects somatic mutations also?
HaplotypeCaller Mutation Exome somatic germline
updated 4.9 years ago by 48k • written 4.9 years ago by ▴ 690
6
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1
reply
2.6k
views
what is the difference between calling variants with and without interval list?
GATK HaplotypeCaller intervallist
updated 4.9 years ago by ▴ 190 • written 4.9 years ago by ▴ 690
0
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1
reply
784
views
How to interpret the values given in the BisoGenet output table ?
BisoGenet protein interction nework Cytoscape
updated 4.9 years ago by ▴ 650 • written 4.9 years ago by ▴ 690
1
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0
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778
views
How to extract list of proteins delectable by immune histochemistry?
Immune Histochemistry IHC detection cancer
4.9 years ago by svp ▴ 690
1
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0
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1.1k
views
Comment: C: Calculation of Mentha Score
4.9 years ago by svp ▴ 690
2
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0
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1.3k
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Answer: A: How to perform batch correction when we have only single condition?
4.9 years ago by svp ▴ 690
5
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2
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1.3k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 14 months ago by 45k • written 4.9 years ago by ▴ 690
0
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1
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4.7k
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Comment: C: Normalization of RNASeq read counts without conditions
4.9 years ago by svp ▴ 690
8
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1
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2.1k
views
How can I call both somatic and germline variants from bam file?
exome variant calling somatic germline ngs
updated 4.9 years ago by ▴ 90 • written 4.9 years ago by ▴ 690
0
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1
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45k
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Answer: A: Converting a VCF with SNPs and indels to BED format
5.0 years ago by svp ▴ 690
0
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0
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1.5k
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Comment: C: Why snpEff annotates same region with different "effects" and why some effects a
5.0 years ago by svp ▴ 690
0
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1
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1.5k
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Comment: C: Why snpEff annotates same region with different "effects" and why some effects a
5.0 years ago by svp ▴ 690
0
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4
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1.5k
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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
5.0 years ago by svp ▴ 690
2
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1
reply
898
views
How to convert genomic region of following type to vcf file?
VCF Conversion LiftOver
updated 5.0 years ago by 166k • written 5.0 years ago by ▴ 690
5
votes
4
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9.1k
views
Why 'filterByExpr' does not eliminate low read counts from the expression data?
edgeR RNA-Seq DEGs filterByExpr
updated 5.1 years ago by ★ 8.2k • written 5.1 years ago by ▴ 690
3
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0
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2.9k
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Answer: A: How do I run a .fastq single-end file in rsem-calculate-expression?
5.2 years ago by svp ▴ 690
3
votes
1
reply
3.6k
views
What is the difference of output samtools depth and samtools view -c on location of bam file?
samtools depth count bam
updated 5.3 years ago by ★ 1.3k • written 5.3 years ago by ▴ 690
1
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0
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1.4k
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Answer: A: How to get reference genome sequence given species name
5.3 years ago by svp ▴ 690
0
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0
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4.2k
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Answer: A: depth calculation for targeted resequencing
5.3 years ago by svp ▴ 690
0
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0
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14k
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Comment: C: Compute mean depth coverage for exome data with paired end, overlapping, feature
5.3 years ago by svp ▴ 690
0
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1
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14k
views
Comment: C: Compute mean depth coverage for exome data with paired end, overlapping, feature
5.3 years ago by svp ▴ 690
0
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1
reply
14k
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Comment: C: Compute mean depth coverage for exome data with paired end, overlapping, feature
5.3 years ago by svp ▴ 690
0
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1
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263k
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Comment: C: Tools To Calculate Average Coverage For A Bam File?
5.3 years ago by svp ▴ 690
0
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1
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1.0k
views
How to extract coverage of custom target regions (bed file) from a bam file?
coverage bedtools
5.3 years ago by svp ▴ 690
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