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5
votes
2
replies
884
views
Fastq: how can I check if they are from DNA or RNAseq data?
WES Fastq
updated 22 months ago by ★ 5.1k • written 22 months ago by ▴ 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 3.7 years ago by ▴ 310 • written 3.7 years ago by ▴ 680
2
votes
1
reply
1.3k
views
Does HaploypeCaller detects somatic mutations also?
HaplotypeCaller Mutation Exome somatic germline
updated 3.8 years ago by 47k • written 3.8 years ago by ▴ 680
6
votes
1
reply
2.2k
views
what is the difference between calling variants with and without interval list?
GATK HaplotypeCaller intervallist
updated 3.8 years ago by ▴ 170 • written 3.8 years ago by ▴ 680
0
votes
1
reply
626
views
How to interpret the values given in the BisoGenet output table ?
BisoGenet protein interction nework Cytoscape
updated 3.8 years ago by ▴ 620 • written 3.8 years ago by ▴ 680
1
vote
0
replies
682
views
How to extract list of proteins delectable by immune histochemistry?
Immune Histochemistry IHC detection cancer
3.8 years ago by svp ▴ 680
5
votes
2
replies
1.1k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 29 days ago by 43k • written 3.8 years ago by ▴ 680
6
votes
1
reply
1.8k
views
How can I call both somatic and germline variants from bam file?
exome variant calling somatic germline ngs
updated 3.8 years ago by ▴ 70 • written 3.8 years ago by ▴ 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
3.9 years ago by svp ▴ 680
2
votes
1
reply
738
views
How to convert genomic region of following type to vcf file?
VCF Conversion LiftOver
updated 3.9 years ago by 161k • written 3.9 years ago by ▴ 680
5
votes
4
replies
8.0k
views
Why 'filterByExpr' does not eliminate low read counts from the expression data?
edgeR RNA-Seq DEGs filterByExpr
updated 4.0 years ago by ★ 7.2k • written 4.0 years ago by ▴ 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 4.2 years ago by ★ 1.2k • written 4.2 years ago by ▴ 680
0
votes
1
reply
804
views
How to extract coverage of custom target regions (bed file) from a bam file?
coverage bedtools
4.2 years ago by svp ▴ 680
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