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813
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Clarification on StringTie's `--merge` parameters
stringtie stringtie-merge
updated 9 weeks ago by • 0 • written 9 months ago by ▴ 290
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515
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Comment: Comment: Feature Counts: low assigned alignments (1.9%) with -s 0: Unstranded option any
4 months ago by DGTool ▴ 290
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1
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703
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Comment: Comment: genome annotation and GFF file formation
4 months ago by DGTool ▴ 290
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2
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703
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Comment: Comment: genome annotation and GFF file formation
4 months ago by DGTool ▴ 290
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1.4k
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Comment: Comment: How to do datamining in bioinformatics
4 months ago by DGTool ▴ 290
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658
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Comment: Comment: how to find the number of exome bases covered in bam file
4 months ago by DGTool ▴ 290
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658
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Comment: Comment: how to find the number of exome bases covered in bam file
4 months ago by DGTool ▴ 290
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351
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Comment: Comment: only ~12% of assigned reads on featurecount
4 months ago by DGTool ▴ 290
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367
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Answer: Answer: Selection Pressure Analysis
4 months ago by DGTool ▴ 290
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675
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Comment: Comment: Are tens of DEGs still biologically meaningful?
4 months ago by DGTool ▴ 290
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1.2k
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Comment: Comment: featureCounts segmentation fault
4 months ago by DGTool ▴ 290
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856
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Answer: Answer: Problem obtaining RNA-seq counts for whole gene (intron and exon), exon only, an
4 months ago by DGTool ▴ 290
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1
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1.5k
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Comment: Comment: RNA-Seq mutation calling without germline data
4 months ago by DGTool ▴ 290
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1
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707
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Comment: Comment: Genome Assembly Workflow assessment
4 months ago by DGTool ▴ 290
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1
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1.5k
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Answer: Answer: RNA-Seq mutation calling without germline data
4 months ago by DGTool ▴ 290
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0
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784
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Comment: Comment: Structural Variants (SV) Manta output interpretation
4 months ago by DGTool ▴ 290
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1
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784
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Answer: Answer: Structural Variants (SV) Manta output interpretation
4 months ago by DGTool ▴ 290
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779
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Comment: Comment: What type of graph or visualization would be most appropriate to represent this
5 months ago by DGTool ▴ 290
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1
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497
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Answer: Answer: gatk-funcotator data source
5 months ago by DGTool ▴ 290
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1
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690
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Answer: Answer: remove the letter a from a biplot in ggplot
5 months ago by DGTool ▴ 290
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451
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Comment: Comment: Weird correlation between RIP-seq replicates
5 months ago by DGTool ▴ 290
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2
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982
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Answer: Answer: Books and Blogs guiding the programming practice in bioformatic research?
6 months ago by DGTool ▴ 290
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1
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396
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Comment: Comment: Seeking Opinions on Pipeline for Detecting Somatic Variants and Rare Germline Mu
6 months ago by DGTool ▴ 290
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1
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557
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Answer: Answer: PROVEAN input for stop codon
7 months ago by DGTool ▴ 290
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0
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262
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Confusion about StringTie
stringtie
updated 7 months ago by 44k • written 7 months ago by ▴ 290
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1
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864
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Comment: Comment: Hmisc Package error
7 months ago by DGTool ▴ 290
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1
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864
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Answer: Answer: Hmisc Package error
7 months ago by DGTool ▴ 290
1
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2
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1.4k
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Comment: Comment: Nextflow process not executinhg
7 months ago by DGTool ▴ 290
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1
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774
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Comment: Comment: How to find genes with altered CNV from CNVkit output?
7 months ago by DGTool ▴ 290
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1
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1.0k
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Comment: Comment: How to Plot Heatmap for Lower Triangular Matrix Using R
7 months ago by DGTool ▴ 290
2
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1
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774
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Answer: Answer: How to find genes with altered CNV from CNVkit output?
7 months ago by DGTool ▴ 290
0
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0
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567
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Comment: Comment: CNVkit heatmap RAM and Runtime
8 months ago by DGTool ▴ 290
0
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0
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341
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Comment: Comment: How to Predict Drug Targets Using Single-Sample RNA-Seq Data?
8 months ago by DGTool ▴ 290
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1
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1.0k
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Comment: Comment: BAM File Quality Sequences Are "?" and File Size is Very Small After STAR Alignm
8 months ago by DGTool ▴ 290
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1
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1.6k
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Comment: Comment: Ensembl IDs <-> Gene Symbols mapping -- Using org.Hs.eg.db, biomaRt or EnsDb.Hsa
8 months ago by DGTool ▴ 290
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1
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1.6k
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Comment: Comment: Ensembl IDs <-> Gene Symbols mapping -- Using org.Hs.eg.db, biomaRt or EnsDb.Hsa
8 months ago by DGTool ▴ 290
2
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7
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1.6k
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Ensembl IDs <-> Gene Symbols mapping -- Using org.Hs.eg.db, biomaRt or EnsDb.Hsapiens.v86?
org.hs.eg.db EnsDb.Hsapiens.v86 biomaRt ensembl
updated 8 months ago by ▴ 430 • written 8 months ago by ▴ 290
0
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0
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308
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Using CNVkit for checking normal samples
CNV cnvkit
8 months ago by DGTool ▴ 290
1
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0
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365
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Answer: Answer: Alternative Database for Somatic Indel Realignment (COSMIC Alternative)
8 months ago by DGTool ▴ 290
0
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1
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735
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Comment: Comment: GATK Structural Variants Pipeline - Steps
9 months ago by DGTool ▴ 290
0
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0
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249
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Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell communication ligand-receptor self-regulation
9 months ago by DGTool ▴ 290
0
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1
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1.2k
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Answer: Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
9 months ago by DGTool ▴ 290
0
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0
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531
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Comment: Comment: perseus software (version 1.5.5)
9 months ago by DGTool ▴ 290
2
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0
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755
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Answer: Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
9 months ago by DGTool ▴ 290
0
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0
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948
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Comment: Comment: Pluritest for pluripotency broken
9 months ago by DGTool ▴ 290
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1
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3.9k
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Comment: Comment: CNVKIT - unable to produce scatter and diagram pdfs
9 months ago by DGTool ▴ 290
0
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0
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337
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Confusion with somatic variant calling: Advice on Ensembl-compatible resources?
GATK Mutect2 ensembl
10 months ago by DGTool ▴ 290
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