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Batch-correction of partially confounded RNA-seq data
RNA-Seq
updated 3.6 years ago by 8.8k • written 3.6 years ago by ★ 3.5k
18
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12
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6.5k
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Removal of repeat and blacklist regions from ChIP-seq data
ChIP-Seq Blacklist ENCODE
updated 3.6 years ago by 20 • written 7.6 years ago by ★ 3.5k
5
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1
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3.6k
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Answer: C: Batch correction in scRNA-seq data via fastMNN | pro/contra
4.4 years ago by James Ashmore ★ 3.5k
1
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1
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3.4k
views
Answer: A: Help: do I always have to re-open sequence file within a for loop in python?
updated 4.7 years ago by 44k • written 8.7 years ago by ★ 3.5k
0
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1
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3.6k
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Answer: A: KeyError in MACS2
updated 4.7 years ago by 44k • written 8.7 years ago by ★ 3.5k
1
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0
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3.1k
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Answer: A: How to generate random intervals for human genome which do not have overlap with
updated 4.8 years ago by 44k • written 8.7 years ago by ★ 3.5k
1
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1
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4.9k
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Comment: C: why my txt file is empty???? help me please
updated 4.9 years ago by 44k • written 9.0 years ago by ★ 3.5k
0
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0
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6.9k
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Comment: C: compare and search a list of ids in two text file
updated 4.9 years ago by 44k • written 9.0 years ago by ★ 3.5k
0
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0
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3.1k
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Answer: A: Getting coverage per barcode from bamfile with barcoded reads
updated 4.9 years ago by 44k • written 9.1 years ago by ★ 3.5k
0
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0
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1.9k
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Answer: A: genomeCoverageBed out > mapping out
updated 4.9 years ago by 44k • written 9.1 years ago by ★ 3.5k
0
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1
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7.2k
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Comment: C: Sublime Text 2: Output Error After I Installed Anaconda
updated 4.9 years ago by 44k • written 9.2 years ago by ★ 3.5k
9
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1
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5.3k
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Answer: A: Fix SAM flags on quality filtered paired-end BAM file
updated 4.9 years ago by 44k • written 9.2 years ago by ★ 3.5k
2
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1
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2.2k
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Answer: A: How to retrive the number of reads aligned to various genomic features?
updated 4.9 years ago by 44k • written 9.3 years ago by ★ 3.5k
9
votes
14
replies
11k
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Normalising ChIP-seq data to RPM using a 1 or 2 count for paired-end data?
ChIP-Seq normalisation paired-end
updated 2.4 years ago by 44k • written 9.6 years ago by ★ 3.5k
0
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0
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4.8k
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Comment: C: Software to extract run information from FASTQ headers?
5.6 years ago by James Ashmore ★ 3.5k
1
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0
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4.8k
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Comment: C: Software to extract run information from FASTQ headers?
5.6 years ago by James Ashmore ★ 3.5k
7
votes
8
replies
4.8k
views
Software to extract run information from FASTQ headers?
fastq
updated 5.6 years ago by 163k • written 5.6 years ago by ★ 3.5k
0
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0
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4.8k
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Comment: C: Software to extract run information from FASTQ headers?
5.6 years ago by James Ashmore ★ 3.5k
1
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2
replies
2.2k
views
Experimental design for RNA-seq time-course with the same start and end points but different treatments
RNA-Seq
updated 5.9 years ago by 20 • written 6.0 years ago by ★ 3.5k
0
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1
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3.3k
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Comment: C: So frustrated compiling necessary packages in a linux system
5.9 years ago by James Ashmore ★ 3.5k
0
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0
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3.5k
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Answer: A: Finding differences in motif enrichment between ATAC peak samples?
5.9 years ago by James Ashmore ★ 3.5k
0
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0
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2.2k
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Comment: C: Experimental design for RNA-seq time-course with the same start and end points b
6.0 years ago by James Ashmore ★ 3.5k
1
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0
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7.2k
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Answer: A: mitochondrial blacklists ATAC-Seq
updated 6.0 years ago by 44k • written 8.6 years ago by ★ 3.5k
2
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1
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4.2k
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Comment: C: using bash variable in picard MarkDuplicates command
6.2 years ago by James Ashmore ★ 3.5k
1
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0
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3.8k
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Comment: C: Analysis of gene expression data
6.2 years ago by James Ashmore ★ 3.5k
2
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0
replies
4.4k
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Answer: A: Processing ATAC-seq data after peak calling
6.2 years ago by James Ashmore ★ 3.5k
0
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1
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3.0k
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Comment: C: A question about Homer ChIP-seq analysis
6.3 years ago by James Ashmore ★ 3.5k
0
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1
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3.0k
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Comment: C: A question about Homer ChIP-seq analysis
6.3 years ago by James Ashmore ★ 3.5k
0
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1
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7.2k
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Comment: C: Annotating/Finding "NNNNNN" scaffold gaps in genome assembly
6.3 years ago by James Ashmore ★ 3.5k
2
votes
1
reply
14k
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Comment: C: ATAC-seq DE analysis
6.3 years ago by James Ashmore ★ 3.5k
0
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1
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3.2k
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Comment: C: Creating pseudo-replicates from a paired-end BAM file
6.3 years ago by James Ashmore ★ 3.5k
0
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1
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3.2k
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Comment: C: Creating pseudo-replicates from a paired-end BAM file
6.3 years ago by James Ashmore ★ 3.5k
18
votes
1
reply
38k
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Answer: A: output TMM normalized counts with edgeR
6.3 years ago by James Ashmore ★ 3.5k
0
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1
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38k
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Comment: C: output TMM normalized counts with edgeR
6.3 years ago by James Ashmore ★ 3.5k
3
votes
1
reply
3.9k
views
Answer: A: ATAC-seq : strategies to have the list of the expressed genes
6.4 years ago by James Ashmore ★ 3.5k
0
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1
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3.9k
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Comment: C: ATAC-seq : strategies to have the list of the expressed genes
6.4 years ago by James Ashmore ★ 3.5k
0
votes
0
replies
1.2k
views
Measuring insertion/deletion frequency of a small sequence motif
SNP MNP
6.4 years ago by James Ashmore ★ 3.5k
1
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1
reply
4.5k
views
Comment: C: Diffbind - Very high proportion of significant peaks
6.5 years ago by James Ashmore ★ 3.5k
0
votes
1
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1.8k
views
Extract genomic feature related to point from mean-variance plot in limma/voom
limma voom
updated 6.5 years ago by 35k • written 8.2 years ago by ★ 3.5k
0
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0
replies
1.6k
views
Answer: A: Error in BioMartVersion
6.6 years ago by James Ashmore ★ 3.5k
2
votes
0
replies
3.3k
views
Comment: C: Utility of Kallisto bootstraps when not using sleuth downstream
6.7 years ago by James Ashmore ★ 3.5k
2
votes
1
reply
6.0k
views
Comment: C: converting paired end reads to single end, is this a good idea?
6.7 years ago by James Ashmore ★ 3.5k
0
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0
replies
1.1k
views
Comment: C: Please share a link of an article on Transcriptomic analysis
6.7 years ago by James Ashmore ★ 3.5k
0
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2
replies
6.0k
views
Comment: C: converting paired end reads to single end, is this a good idea?
6.7 years ago by James Ashmore ★ 3.5k
1
vote
0
replies
2.5k
views
Comment: C: Normalizing transcriptome data by tissue type
6.7 years ago by James Ashmore ★ 3.5k
1
vote
1
reply
4.4k
views
Answer: A: Parse FASTQC data
6.7 years ago by James Ashmore ★ 3.5k
5
votes
2
replies
4.1k
views
Comment: C: Is possible to convert BSgenome object to GRange?
6.7 years ago by James Ashmore ★ 3.5k
2
votes
1
reply
3.6k
views
Comment: C: Changes log2FC values of DESeq2
6.7 years ago by James Ashmore ★ 3.5k
1
vote
1
reply
9.1k
views
Comment: C: High Speed Downloading of SRA, SAM and Fastq Files
6.7 years ago by James Ashmore ★ 3.5k
0
votes
1
reply
1.9k
views
Comment: C: Generate artificial reads
6.8 years ago by James Ashmore ★ 3.5k
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