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• Any tools for predicting binding affinity between TCR and epitode?
• Method to detect genome doubling
• Can we get absolute abundance of TCR using TCR-Seq?
• Shannon vs Simpson for TCR diversity estimation
• Why did expression based subtypng of breast cancer gain much more acceptance than others
• Treat methylation as binary or continuous signal when detecting DMR?
• Is definition of differentially methylated region (DMR) biologically meaningful?
• Why NB distribution is preferred in RNA-Seq while normal distribution is preferred in microarray?
• Logit-normal distribution to model variation among biological replicates
• Identifying zygosity of somatic deletion
• In PCA on RNA-Seq data, what does Gaussian distribution refer to?
• Why can we still be able to continuously discover new cancer driver bioinformatically these days?
• non-reference allele didn't be called into vcf by HC
• Archieve of homologous nucleotide sequence across genome
• Library size normalization during CNV calling from genomically doubled tumor tissue
• Noisy CNV background in old FFPE sample
• Effect size in power analysis when dealing with Poisson based variant caller
• Why methylation sequencing requires much less sequencing depth than DNA-Seq?
• Mutated gene based pathway enrichment
• Why can't use t-test for differential expression (negative binomial distribution assumed)
• Multiple testing correction issue
• Is linearity maintained in linear regression of RNA-Seq?
• Why use LASSO / elastic net in survival regression?
• why PCA for RNA-Seq but tSNE for scRNA-seq?
• Can remote, but same type, tissue be used as RNA-Seq normal control for tumor study?
• Why NMF for mutation signature analysis
• Gene expression distribution (non-DE and DE)
• Would different enrichment tools result differently by defining pathway differently
• Any tools to estimate the relative abundance of immune cell in tumor
• Driver mutation vs biomarker vs recurrent mutation
• SciClone: Why cluster in non-CN neutral region considering it infers only on CN neutral region
• STAR-HT-Seq/featureCount got much more gene expression count than RSEM did
• Inconsistency of allele depth in BAM and VCF
• CBS in CNV calling
• How 2-channel sequencing chemistry (Next-Seq) distinguish "G" and 'no signal'
• one sample from pool shows low quality at the end, why?
• WGS coverage (depth) for CNV detection
• Reads aligning in unstranded RNA-Seq library
• what cause poly-G from NextSeq
• ExAC includes WES of phenotyped population
• Is DNA or RNA better to get somatic mutation profile for neoantigen estimation?
• Infer somatic mutations without normal control
• pipeline for neo-antigen identification
• Fragment size and insert size
• Why CNV calling using VarScan need two steps of fragments merging?
• Can phasing or pre-phase during basecall cause indel?
• Two confusion in bam format
• Why perfectly match (150M) records are not primary alignment in SAM
• A confusion regarding haplotype
• What kind of advantage does PEAR bring?
• Do multiple SNPs exist in same chromosome to be called allele?
• Will random hexamer priming introduce SNP / SNV detection bias?
• Detecting CNV can't cover aneuploidy situation
• STAR genomeLoad issue
• Distribution of somatic mutation
• Detecting variants at very low fractions from ctDNA
• Call variant from RNA-Seq data using Haplotypecaller