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360
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Answer:
Answer: STAR --sjdbGTFfile in alignment step
11 months ago by
dsull
★ 7.2k
1
vote
1
reply
688
views
Answer:
Answer: scRNAseq output generated using STARsolo has gene_id rather than gene_name
11 months ago by
dsull
★ 7.2k
4
votes
1
reply
830
views
Answer:
Answer: How I should set `STAR` parameters to keep all the intronic reads?
11 months ago by
dsull
★ 7.2k
3
votes
0
replies
950
views
Answer:
Answer: Would reaching out to local labs and startups help with my career transition?
12 months ago by
dsull
★ 7.2k
0
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0
replies
1.1k
views
Answer:
Answer: Making PCA plot using variance instead of counts on Sleuth (plot_pca)
updated 12 months ago by
Ram
44k • written 12 months ago by
dsull
★ 7.2k
0
votes
0
replies
447
views
Answer:
Answer: Using tophat2 output for kallisto
12 months ago by
dsull
★ 7.2k
2
votes
1
reply
741
views
Answer:
Answer: bulk seq vs. sc-seq
12 months ago by
dsull
★ 7.2k
0
votes
1
reply
1.2k
views
Answer:
Answer: Differential expression analysis with very high duplication rate
12 months ago by
dsull
★ 7.2k
1
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0
replies
707
views
Answer:
Answer: How to do DESeq2 on Kallisto Data
12 months ago by
dsull
★ 7.2k
3
votes
1
reply
1.4k
views
Answer:
Answer: RNA seq, correlation, gene expression, STAR count
12 months ago by
dsull
★ 7.2k
1
vote
1
reply
2.0k
views
Answer:
Answer: I would like to exclude rRNA in RSEM and quantify it.
13 months ago by
dsull
★ 7.2k
3
votes
1
reply
602
views
Answer:
Answer: Using Expression of a Gene as a Linear Regression Variable
13 months ago by
dsull
★ 7.2k
2
votes
1
reply
828
views
Answer:
Answer: STAR index generation killed after "inserting junctions into the genome indices"
updated 13 months ago by
ATpoint
87k • written 13 months ago by
dsull
★ 7.2k
1
vote
1
reply
911
views
Answer:
Answer: Kallisto-Bustools Output prpblems
14 months ago by
dsull
★ 7.2k
2
votes
1
reply
1.1k
views
Answer:
Answer: Kallisto-bustools output to Seurat Object
14 months ago by
dsull
★ 7.2k
0
votes
1
reply
1.4k
views
Answer:
Answer: bwa-mem reproducibility
14 months ago by
dsull
★ 7.2k
4
votes
1
reply
2.1k
views
Answer:
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
14 months ago by
dsull
★ 7.2k
1
vote
1
reply
1.0k
views
Answer:
Answer: Should SMART-seq2 data be deduplicated in STAR?
14 months ago by
dsull
★ 7.2k
0
votes
1
reply
934
views
Answer:
Answer: Three questions about datasets
15 months ago by
dsull
★ 7.2k
2
votes
1
reply
1.1k
views
Answer:
Answer: Smart seq3 analysis
15 months ago by
dsull
★ 7.2k
2
votes
0
replies
1.1k
views
Answer:
Answer: salmon for gene expression quantification
15 months ago by
dsull
★ 7.2k
1
vote
1
reply
1.3k
views
Answer:
Answer: Quality filtering prior to pseudoalignment
15 months ago by
dsull
★ 7.2k
3
votes
1
reply
1.1k
views
Answer:
Answer: Why am I getting different results with kallisto?
15 months ago by
dsull
★ 7.2k
1
vote
0
replies
524
views
Answer:
Answer: Intenger encoding versus one-hot encoding for chromosome as a predictor in a neu
16 months ago by
dsull
★ 7.2k
1
vote
1
reply
1.6k
views
Answer:
Answer: Best command line tool for downloading sequencing reads
16 months ago by
dsull
★ 7.2k
0
votes
1
reply
724
views
Answer:
Answer: GSEA analysis for phosphoproteins
16 months ago by
dsull
★ 7.2k
1
vote
1
reply
1.2k
views
Answer:
Answer: How to assign gene names after kallisto when I add GFP?
16 months ago by
dsull
★ 7.2k
1
vote
0
replies
2.3k
views
Answer:
Answer: Unmapped Reads in Kallisto
16 months ago by
dsull
★ 7.2k
0
votes
1
reply
1.6k
views
Answer:
Answer: Can one sample t.test be used to determine statistical significance for log2FC v
17 months ago by
dsull
★ 7.2k
0
votes
0
replies
2.1k
views
Answer:
Answer: Is Bioinformatics a Professional Degree?
17 months ago by
dsull
★ 7.2k
2
votes
1
reply
694
views
Answer:
Answer: Is it possible to detect fusion genes by either stranded or unstranded RNA-seq?
18 months ago by
dsull
★ 7.2k
0
votes
1
reply
715
views
Answer:
Answer: Extracting RNA sequence - single cell
18 months ago by
dsull
★ 7.2k
1
vote
1
reply
1.5k
views
Answer:
Answer: Problem creating salmon index
19 months ago by
dsull
★ 7.2k
1
vote
2
replies
967
views
Answer:
Answer: Where can I find the --chromosomes file for kallisto?
19 months ago by
dsull
★ 7.2k
1
vote
1
reply
1.1k
views
Answer:
Answer: MAGeCK MLE's sgRNA efficacies always end up at 1.0
19 months ago by
dsull
★ 7.2k
1
vote
1
reply
2.4k
views
Answer:
Answer: Threshold for a value of RPKM considered significant
19 months ago by
dsull
★ 7.2k
2
votes
1
reply
881
views
Answer:
Answer: How to convert Kallisto output to Salmon?
20 months ago by
dsull
★ 7.2k
1
vote
1
reply
2.4k
views
Answer:
Answer: bar chart to show a p value of 0
20 months ago by
dsull
★ 7.2k
2
votes
2
replies
2.3k
views
Answer:
Answer: No expression found with Salmon and Kallisto
20 months ago by
dsull
★ 7.2k
0
votes
0
replies
563
views
Answer:
Answer: Appropriate RPKM cutoff
20 months ago by
dsull
★ 7.2k
0
votes
0
replies
1.1k
views
Answer:
Answer: How to generate cDNA file from genome FASTA and GTF?
21 months ago by
dsull
★ 7.2k
4
votes
2
replies
1.8k
views
Answer:
Answer: Genes' fpkm values through cufflink
21 months ago by
dsull
★ 7.2k
0
votes
0
replies
581
views
Answer:
Answer: Is it possible to use pseudoalignments.bam to run rMATs?
23 months ago by
dsull
★ 7.2k
2
votes
0
replies
1.2k
views
Answer:
Answer: Confused on strandedness, what are antisense transcripts?
23 months ago by
dsull
★ 7.2k
1
vote
1
reply
1.1k
views
Answer:
Answer: Multiple samples and species with kallisto bus(tools)
23 months ago by
dsull
★ 7.2k
1
vote
1
reply
1.8k
views
Answer:
Answer: STARsolo
23 months ago by
dsull
★ 7.2k
1
vote
1
reply
1.4k
views
Answer:
Answer: kallisto -s o error
23 months ago by
dsull
★ 7.2k
1
vote
0
replies
750
views
Answer:
Answer: Do indexes made with cDNA fasta file contain only mRNAs?
23 months ago by
dsull
★ 7.2k
6
votes
1
reply
1.2k
views
Answer:
Answer: Question about aggregating p values from different DE analysis methods for the s
23 months ago by
dsull
★ 7.2k
1
vote
2
replies
5.1k
views
Answer:
Answer: How do one analyze data from SMART-Seq stranded kit (v4)?
24 months ago by
dsull
★ 7.2k
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