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Answer: Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
1 day ago by swbarnes2 14k
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323
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Answer: Answer: Sequence read length shorter than flow cell specification
9 days ago by swbarnes2 14k
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289
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Answer: Answer: from row count to tpm
12 days ago by swbarnes2 14k
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892
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Answer: Answer: Adding CB tag to bam file
16 days ago by swbarnes2 14k
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684
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Answer: Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
17 days ago by swbarnes2 14k
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604
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Answer: Answer: Removing adapter/primer sequence from reads while keeping flanking regions
4 weeks ago by swbarnes2 14k
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331
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Answer: Answer: Find out shared differentially expressed genes between two cell lines due to kno
6 weeks ago by swbarnes2 14k
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302
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Answer: Answer: Detecting viruses in human rna seq data
6 weeks ago by swbarnes2 14k
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418
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Answer: Answer: Is it better to pool samples prior to running deseq2, or should the algorithm be
6 weeks ago by swbarnes2 14k
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561
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Answer: Answer: Overriding a color palette in R to emphasize specific data points
7 weeks ago by swbarnes2 14k
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576
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Answer: Answer: RNA_seq
7 weeks ago by swbarnes2 14k
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371
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Answer: Answer: Is it feasible to merge Illumina RNA-Seq data with varying read lengths?
7 weeks ago by swbarnes2 14k
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381
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Answer: Answer: Re. Batch effect correction in data with a design matrix without full rank
8 weeks ago by swbarnes2 14k
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537
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Answer: Answer: RNA Seq Sample Outlier
8 weeks ago by swbarnes2 14k
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402
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Answer: Answer: STAR alignment setting for RNA-Seq data from mouse background expressing a human
8 weeks ago by swbarnes2 14k
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451
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Answer: Answer: (STAR) What causes a high number of reads that are unmapped because they are too
8 weeks ago by swbarnes2 14k
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314
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Answer: Answer: Single cell rna sequencing analysis using R help
8 weeks ago by swbarnes2 14k
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424
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Answer: Answer: single cell rna seq-how to DEG analyze??(full code & Dimplot added)
8 weeks ago by swbarnes2 14k
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250
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Answer: Answer: biological replicate in STAR command
9 weeks ago by swbarnes2 14k
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391
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Answer: Answer: PCA plot analysis
9 weeks ago by swbarnes2 14k
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448
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Answer: Answer: ENA fastq file shown as single-end but has 2 fastq files: X.fastq.gz and Y.fastq
10 weeks ago by swbarnes2 14k
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574
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Answer: Answer: Trouble Understanding DESeq2 Design Formula ("Model Matrix is not Full Rank")
12 weeks ago by swbarnes2 14k
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571
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Answer: Answer: Help interpreting Samtools Flagstat results
3 months ago by swbarnes2 14k
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462
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Answer: Answer: Running Deseq2 with all samples vs samples for each comparison separately
3 months ago by swbarnes2 14k
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327
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Answer: Answer: Interpretation of output from MiXCR TCR sequencing
4 months ago by swbarnes2 14k
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364
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Answer: Answer: Strand information from reverse stranded RNA-seq
4 months ago by swbarnes2 14k
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637
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Answer: Answer: bcl2fastq problems with the yield
4 months ago by swbarnes2 14k
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483
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Answer: Answer: Are 10x cellranger-arc ATAC bam files deduplicated?
5 months ago by swbarnes2 14k
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400
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Answer: Answer: Bulk and Single Cell RNA-seq online course
5 months ago by swbarnes2 14k
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827
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Answer: Answer: STAR ALIGNMENT
5 months ago by swbarnes2 14k
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953
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Answer: Answer: Handling multiple fastq files per sample, per lane, per read out of the Cellrang
5 months ago by swbarnes2 14k
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757
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Answer: Answer: RNAseq how to map Mouse+Virus Genome with STAR
5 months ago by swbarnes2 14k
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746
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Answer: Answer: batch correction in DESeq2
6 months ago by swbarnes2 14k
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465
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Answer: Answer: Help with DESeq2 Analysis of Multiple Conditions
6 months ago by swbarnes2 14k
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756
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Answer: Answer: DESeq2: DESeqDataSetFromMatrix Error
7 months ago by swbarnes2 14k
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904
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Answer: Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
7 months ago by swbarnes2 14k
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759
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Answer: Answer: DESeq2 analysis using two featureCounts generated from different studies
7 months ago by swbarnes2 14k
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1.1k
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Answer: Answer: Adding a control sample to bulk RNA-seq
7 months ago by swbarnes2 14k
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525
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Answer: Answer: DESeq2 design comparing changes through 2 timepoints of 2 different treatments.
7 months ago by swbarnes2 14k
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504
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Answer: Answer: sequencing machines output files layout
7 months ago by swbarnes2 14k
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538
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Answer: Answer: DESeqDataSetFromMatrix error
7 months ago by swbarnes2 14k
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464
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Answer: Answer: Deseq2
7 months ago by swbarnes2 14k
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764
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Answer: Answer: DESEQ2 analysis - PCA plot
9 months ago by swbarnes2 14k
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469
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Answer: Answer: Add gene counts of same samples run on two lanes (Novaseq)
9 months ago by swbarnes2 14k
2
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640
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Answer: Answer: bcl2fastq not recognizing multiple barcode-mismatch argument
9 months ago by swbarnes2 14k
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1.1k
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Answer: Answer: Is RSEM required for RNA-seq data analysis using STAR and edgeR?
9 months ago by swbarnes2 14k
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681
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Answer: Answer: 10x genomics hashtag samples
9 months ago by swbarnes2 14k
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625
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Answer: Answer: DESeq2, Time-course interpretation
10 months ago by swbarnes2 14k
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Answer: Answer: Multiple testing correction in RNA-Seq
10 months ago by swbarnes2 14k
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2.2k
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Answer: Answer: How to create a Seurat object from the `xxx_metadata.txt.gz ` and `xxx_counts.t
10 months ago by swbarnes2 14k
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