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Answer: Answer: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
9 days ago by swbarnes2 13k
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444
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Answer: Answer: DESeq2 analysis using two featureCounts generated from different studies
12 days ago by swbarnes2 13k
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Comment: Comment: Adding a control sample to bulk RNA-seq
12 days ago by swbarnes2 13k
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379
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Comment: Comment: How to DESeq2 using miRNA data obtained using TCGAbiolinks
13 days ago by swbarnes2 13k
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Answer: Answer: Adding a control sample to bulk RNA-seq
14 days ago by swbarnes2 13k
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292
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Comment: Comment: Batch effect consideration (re-seq the same sample twice)
16 days ago by swbarnes2 13k
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250
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Answer: Answer: DESeq2 design comparing changes through 2 timepoints of 2 different treatments.
19 days ago by swbarnes2 13k
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262
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Answer: Answer: sequencing machines output files layout
20 days ago by swbarnes2 13k
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257
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Answer: Answer: DESeqDataSetFromMatrix error
20 days ago by swbarnes2 13k
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265
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Answer: Answer: Deseq2
21 days ago by swbarnes2 13k
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336
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Comment: Comment: htseq-count reports count values for deleted genes
23 days ago by swbarnes2 13k
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416
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Comment: Comment: How to Add Mutations to the sequence
5 weeks ago by swbarnes2 13k
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814
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Comment: Comment: Formatting RNA-Seq Data for Kruskal Wallis Test on R
5 weeks ago by swbarnes2 13k
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462
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Comment: Comment: STAR mapping - regarding output files content
6 weeks ago by swbarnes2 13k
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345
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Comment: Comment: RSEM uses different gene lengths for each sample.
8 weeks ago by swbarnes2 13k
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370
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Answer: Answer: DESEQ2 analysis - PCA plot
8 weeks ago by swbarnes2 13k
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429
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Comment: Comment: Can I extract a complete sequence of gene from mapped reads bam file
9 weeks ago by swbarnes2 13k
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249
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Answer: Answer: Add gene counts of same samples run on two lanes (Novaseq)
10 weeks ago by swbarnes2 13k
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328
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Answer: Answer: bcl2fastq not recognizing multiple barcode-mismatch argument
11 weeks ago by swbarnes2 13k
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653
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Comment: Comment: Is RSEM required for RNA-seq data analysis using STAR and edgeR?
12 weeks ago by swbarnes2 13k
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653
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Answer: Answer: Is RSEM required for RNA-seq data analysis using STAR and edgeR?
12 weeks ago by swbarnes2 13k
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350
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Answer: Answer: 10x genomics hashtag samples
12 weeks ago by swbarnes2 13k
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333
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Answer: Answer: DESeq2, Time-course interpretation
3 months ago by swbarnes2 13k
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Answer: Answer: Multiple testing correction in RNA-Seq
3 months ago by swbarnes2 13k
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933
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Comment: Comment: Transcript quantification
3 months ago by swbarnes2 13k
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1.1k
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Answer: Answer: How to create a Seurat object from the `xxx_metadata.txt.gz ` and `xxx_counts.t
3 months ago by swbarnes2 13k
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1.0k
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Comment: Comment: Getting sequences from fastq file using Grep command
3 months ago by swbarnes2 13k
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1.0k
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Answer: Answer: Getting sequences from fastq file using Grep command
3 months ago by swbarnes2 13k
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955
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Comment: Comment: A question about the raw RNA-seq processing workflow
3 months ago by swbarnes2 13k
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955
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Comment: Comment: A question about the raw RNA-seq processing workflow
3 months ago by swbarnes2 13k
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742
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Answer: Answer: Italicise annotations with pheatmap
4 months ago by swbarnes2 13k
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1.0k
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Comment: Comment: Counting intronic reads in bulk RNA-seq
4 months ago by swbarnes2 13k
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432
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Comment: Comment: Ambient RNA expression correction
4 months ago by swbarnes2 13k
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539
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Answer: Answer: What is the best way to clean bulk RNA-seq data?
4 months ago by swbarnes2 13k
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596
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Comment: Comment: RNAseq Data and Pipeline
4 months ago by swbarnes2 13k
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740
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Comment: Comment: Is there anyway to cancel CPM normalization?
4 months ago by swbarnes2 13k
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917
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Comment: Comment: Single cell chemistry
4 months ago by swbarnes2 13k
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917
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Comment: Comment: Single cell chemistry
4 months ago by swbarnes2 13k
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917
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Comment: Comment: Single cell chemistry
4 months ago by swbarnes2 13k
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917
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Comment: Comment: Single cell chemistry
4 months ago by swbarnes2 13k
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1.0k
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Answer: Answer: Counting intronic reads in bulk RNA-seq
4 months ago by swbarnes2 13k
0
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1
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917
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Answer: Answer: Single cell chemistry
4 months ago by swbarnes2 13k
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0
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351
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Answer: Answer: How to extract out gene specific reads from concatenated fastq file
4 months ago by swbarnes2 13k
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400
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Comment: Comment: Using RNA-seq to detect pathogen sequences in host tissue
4 months ago by swbarnes2 13k
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597
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Answer: Answer: rna seq design matrix
4 months ago by swbarnes2 13k
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312
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Answer: Answer: Different read numbers for the same samples
4 months ago by swbarnes2 13k
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875
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Comment: Comment: On "wings" in volcano plots...
4 months ago by swbarnes2 13k
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1.2k
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Comment: Comment: Subsetting DESeq data set to compare treatments within one group (multi-group ex
4 months ago by swbarnes2 13k
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1.2k
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Answer: Answer: Subsetting DESeq data set to compare treatments within one group (multi-group ex
4 months ago by swbarnes2 13k
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557
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Comment: Comment: How to better distribute my replicates between two batches of bulk RNAseq?
4 months ago by swbarnes2 13k
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