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363
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Answer:
Answer: How should I make kallisto indexes?
1 day ago by
dsull
★ 5.9k
1
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1
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261
views
Answer:
Answer: High Malat-1 expression in single cell data
1 day ago by
dsull
★ 5.9k
0
votes
0
replies
380
views
Answer:
Answer: What does it mean single base resolution in sequencing?
2 days ago by
dsull
★ 5.9k
1
vote
1
reply
662
views
Answer:
Answer: Heatmap and rna-seq
4 days ago by
dsull
★ 5.9k
2
votes
1
reply
322
views
Answer:
Answer: what is the purpose of indexing the reference genome (Kallisto)
4 days ago by
dsull
★ 5.9k
1
vote
2
replies
479
views
Answer:
Answer: To get p-values for the TPM
6 days ago by
dsull
★ 5.9k
2
votes
1
reply
482
views
Answer:
Answer: Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
8 days ago by
dsull
★ 5.9k
0
votes
0
replies
345
views
Answer:
Answer: How to establish haplotype-specific gene expression levels
4 days ago by
dsull
★ 5.9k
1
vote
1
reply
527
views
Answer:
Answer: STARsolo ; Reads are NOT mapped to transcriptome
21 days ago by
dsull
★ 5.9k
1
vote
1
reply
399
views
Answer:
Answer: DESeq2 and normalization
4 weeks ago by
dsull
★ 5.9k
1
vote
1
reply
727
views
Answer:
Answer: cutadapt not trimming all adapters in PE Illumina sequencing
6 weeks ago by
dsull
★ 5.9k
0
votes
1
reply
240
views
Answer:
Answer: DEG (Differential expression gene) analysis
6 weeks ago by
dsull
★ 5.9k
1
vote
0
replies
393
views
Answer:
Answer: scRNAseq normalization
6 weeks ago by
dsull
★ 5.9k
0
votes
0
replies
160
views
Answer:
Answer: STAR --sjdbGTFfile in alignment step
6 weeks ago by
dsull
★ 5.9k
1
vote
1
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295
views
Answer:
Answer: scRNAseq output generated using STARsolo has gene_id rather than gene_name
8 weeks ago by
dsull
★ 5.9k
4
votes
1
reply
369
views
Answer:
Answer: How I should set `STAR` parameters to keep all the intronic reads?
8 weeks ago by
dsull
★ 5.9k
3
votes
0
replies
565
views
Answer:
Answer: Would reaching out to local labs and startups help with my career transition?
9 weeks ago by
dsull
★ 5.9k
0
votes
0
replies
586
views
Answer:
Answer: Making PCA plot using variance instead of counts on Sleuth (plot_pca)
updated 9 weeks ago by
Ram
43k • written 9 weeks ago by
dsull
★ 5.9k
0
votes
0
replies
255
views
Answer:
Answer: Using tophat2 output for kallisto
9 weeks ago by
dsull
★ 5.9k
2
votes
1
reply
381
views
Answer:
Answer: bulk seq vs. sc-seq
11 weeks ago by
dsull
★ 5.9k
0
votes
1
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566
views
Answer:
Answer: Differential expression analysis with very high duplication rate
12 weeks ago by
dsull
★ 5.9k
1
vote
0
replies
387
views
Answer:
Answer: How to do DESeq2 on Kallisto Data
12 weeks ago by
dsull
★ 5.9k
3
votes
1
reply
626
views
Answer:
Answer: RNA seq, correlation, gene expression, STAR count
3 months ago by
dsull
★ 5.9k
1
vote
1
reply
1.1k
views
Answer:
Answer: I would like to exclude rRNA in RSEM and quantify it.
3 months ago by
dsull
★ 5.9k
3
votes
1
reply
325
views
Answer:
Answer: Using Expression of a Gene as a Linear Regression Variable
3 months ago by
dsull
★ 5.9k
2
votes
1
reply
364
views
Answer:
Answer: STAR index generation killed after "inserting junctions into the genome indices"
updated 3 months ago by
ATpoint
82k • written 3 months ago by
dsull
★ 5.9k
1
vote
1
reply
559
views
Answer:
Answer: Kallisto-Bustools Output prpblems
4 months ago by
dsull
★ 5.9k
2
votes
1
reply
571
views
Answer:
Answer: Kallisto-bustools output to Seurat Object
4 months ago by
dsull
★ 5.9k
0
votes
1
reply
777
views
Answer:
Answer: bwa-mem reproducibility
4 months ago by
dsull
★ 5.9k
3
votes
1
reply
1.1k
views
Answer:
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
4 months ago by
dsull
★ 5.9k
1
vote
1
reply
592
views
Answer:
Answer: Should SMART-seq2 data be deduplicated in STAR?
5 months ago by
dsull
★ 5.9k
0
votes
1
reply
623
views
Answer:
Answer: Three questions about datasets
5 months ago by
dsull
★ 5.9k
2
votes
1
reply
646
views
Answer:
Answer: Smart seq3 analysis
5 months ago by
dsull
★ 5.9k
2
votes
0
replies
575
views
Answer:
Answer: salmon for gene expression quantification
5 months ago by
dsull
★ 5.9k
1
vote
1
reply
689
views
Answer:
Answer: Quality filtering prior to pseudoalignment
5 months ago by
dsull
★ 5.9k
3
votes
1
reply
678
views
Answer:
Answer: Why am I getting different results with kallisto?
5 months ago by
dsull
★ 5.9k
1
vote
0
replies
318
views
Answer:
Answer: Intenger encoding versus one-hot encoding for chromosome as a predictor in a neu
6 months ago by
dsull
★ 5.9k
1
vote
1
reply
1.0k
views
Answer:
Answer: Best command line tool for downloading sequencing reads
6 months ago by
dsull
★ 5.9k
0
votes
1
reply
486
views
Answer:
Answer: GSEA analysis for phosphoproteins
6 months ago by
dsull
★ 5.9k
1
vote
1
reply
691
views
Answer:
Answer: How to assign gene names after kallisto when I add GFP?
7 months ago by
dsull
★ 5.9k
1
vote
0
replies
1.8k
views
Answer:
Answer: Unmapped Reads in Kallisto
7 months ago by
dsull
★ 5.9k
0
votes
1
reply
1.1k
views
Answer:
Answer: Can one sample t.test be used to determine statistical significance for log2FC v
8 months ago by
dsull
★ 5.9k
0
votes
0
replies
1.5k
views
Answer:
Answer: Is Bioinformatics a Professional Degree?
8 months ago by
dsull
★ 5.9k
2
votes
1
reply
471
views
Answer:
Answer: Is it possible to detect fusion genes by either stranded or unstranded RNA-seq?
8 months ago by
dsull
★ 5.9k
0
votes
1
reply
539
views
Answer:
Answer: Extracting RNA sequence - single cell
8 months ago by
dsull
★ 5.9k
1
vote
1
reply
908
views
Answer:
Answer: Problem creating salmon index
9 months ago by
dsull
★ 5.9k
1
vote
2
replies
735
views
Answer:
Answer: Where can I find the --chromosomes file for kallisto?
9 months ago by
dsull
★ 5.9k
1
vote
1
reply
701
views
Answer:
Answer: MAGeCK MLE's sgRNA efficacies always end up at 1.0
10 months ago by
dsull
★ 5.9k
1
vote
1
reply
1.7k
views
Answer:
Answer: Threshold for a value of RPKM considered significant
10 months ago by
dsull
★ 5.9k
2
votes
1
reply
608
views
Answer:
Answer: How to convert Kallisto output to Salmon?
10 months ago by
dsull
★ 5.9k
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