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5
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3.4k
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Answer:
C: Batch correction in scRNA-seq data via fastMNN | pro/contra
4.0 years ago by
James Ashmore
★ 3.4k
1
vote
1
reply
3.2k
views
Answer:
A: Help: do I always have to re-open sequence file within a for loop in python?
updated 4.3 years ago by
Ram
43k • written 8.3 years ago by
James Ashmore
★ 3.4k
0
votes
1
reply
3.5k
views
Answer:
A: KeyError in MACS2
updated 4.4 years ago by
Ram
43k • written 8.3 years ago by
James Ashmore
★ 3.4k
1
vote
0
replies
3.0k
views
Answer:
A: How to generate random intervals for human genome which do not have overlap with
updated 4.4 years ago by
Ram
43k • written 8.3 years ago by
James Ashmore
★ 3.4k
0
votes
0
replies
3.0k
views
Answer:
A: Getting coverage per barcode from bamfile with barcoded reads
updated 4.5 years ago by
Ram
43k • written 8.7 years ago by
James Ashmore
★ 3.4k
0
votes
0
replies
1.8k
views
Answer:
A: genomeCoverageBed out > mapping out
updated 4.5 years ago by
Ram
43k • written 8.7 years ago by
James Ashmore
★ 3.4k
8
votes
1
reply
5.1k
views
Answer:
A: Fix SAM flags on quality filtered paired-end BAM file
updated 4.5 years ago by
Ram
43k • written 8.9 years ago by
James Ashmore
★ 3.4k
2
votes
1
reply
2.1k
views
Answer:
A: How to retrive the number of reads aligned to various genomic features?
updated 4.5 years ago by
Ram
43k • written 8.9 years ago by
James Ashmore
★ 3.4k
0
votes
0
replies
3.3k
views
Answer:
A: Finding differences in motif enrichment between ATAC peak samples?
5.6 years ago by
James Ashmore
★ 3.4k
1
vote
0
replies
6.9k
views
Answer:
A: mitochondrial blacklists ATAC-Seq
updated 5.6 years ago by
Ram
43k • written 8.2 years ago by
James Ashmore
★ 3.4k
2
votes
0
replies
4.1k
views
Answer:
A: Processing ATAC-seq data after peak calling
5.9 years ago by
James Ashmore
★ 3.4k
18
votes
1
reply
37k
views
Answer:
A: output TMM normalized counts with edgeR
5.9 years ago by
James Ashmore
★ 3.4k
3
votes
1
reply
3.7k
views
Answer:
A: ATAC-seq : strategies to have the list of the expressed genes
6.0 years ago by
James Ashmore
★ 3.4k
0
votes
0
replies
1.5k
views
Answer:
A: Error in BioMartVersion
6.3 years ago by
James Ashmore
★ 3.4k
1
vote
1
reply
4.1k
views
Answer:
A: Parse FASTQC data
6.3 years ago by
James Ashmore
★ 3.4k
2
votes
1
reply
1.7k
views
Answer:
A: Generate artificial reads
6.4 years ago by
James Ashmore
★ 3.4k
1
vote
1
reply
6.0k
views
Answer:
A: Subset XStringSet by Sequence Name
6.6 years ago by
James Ashmore
★ 3.4k
1
vote
1
reply
3.4k
views
Answer:
A: Use UNIX reverse complement
6.6 years ago by
James Ashmore
★ 3.4k
1
vote
0
replies
2.0k
views
Answer:
A: Conditional modification of counts in the DESeq Data Set
6.6 years ago by
James Ashmore
★ 3.4k
0
votes
1
reply
3.0k
views
Answer:
A: How to delete everything after a certain point in GFF3 file - PYTHON
6.7 years ago by
James Ashmore
★ 3.4k
1
vote
1
reply
3.8k
views
Answer:
A: Data retrieval from GEO
6.7 years ago by
James Ashmore
★ 3.4k
1
vote
2
replies
3.2k
views
Answer:
A: FastQC's report -- 'Per base sequence content' heading odd wave
6.7 years ago by
James Ashmore
★ 3.4k
2
votes
0
replies
1.9k
views
Answer:
A: Design qpcr primers
6.7 years ago by
James Ashmore
★ 3.4k
9
votes
0
replies
9.9k
views
Answer:
A: What "chrUn" stand for in UCSC genome browser web server?
6.7 years ago by
James Ashmore
★ 3.4k
2
votes
0
replies
3.3k
views
Answer:
A: find genes name of a specific location
6.8 years ago by
James Ashmore
★ 3.4k
4
votes
0
replies
3.9k
views
Answer:
A: How to extend bed intervals to a uniform size?
6.8 years ago by
James Ashmore
★ 3.4k
2
votes
2
replies
4.7k
views
Answer:
A: macs2 normalization on broadPeak
6.8 years ago by
James Ashmore
★ 3.4k
6
votes
3
replies
3.9k
views
Answer:
A: Calculate the fraction of genome that is feature X
6.8 years ago by
James Ashmore
★ 3.4k
1
vote
0
replies
1.9k
views
Answer:
A: Add head to coverage output for many files
6.8 years ago by
James Ashmore
★ 3.4k
0
votes
1
reply
2.2k
views
Answer:
A: Need to extract sequences from genome fasta (SeqIO object) into output file usin
6.8 years ago by
James Ashmore
★ 3.4k
1
vote
0
replies
4.6k
views
Answer:
A: Duplicates in ATAC-seq data
6.8 years ago by
James Ashmore
★ 3.4k
1
vote
0
replies
2.1k
views
Answer:
A: retrieve Sequence by Gene name?
6.8 years ago by
James Ashmore
★ 3.4k
1
vote
1
reply
2.3k
views
Answer:
A: Download SRA data via SRA Toolkit.
6.8 years ago by
James Ashmore
★ 3.4k
1
vote
1
reply
4.2k
views
Answer:
A: Differential expression for two very different samples
6.8 years ago by
James Ashmore
★ 3.4k
2
votes
2
replies
11k
views
Answer:
A: How to download metadata from the SRA?
6.8 years ago by
James Ashmore
★ 3.4k
4
votes
1
reply
8.8k
views
Answer:
C: Getting average fragment length for single end reads
7.0 years ago by
James Ashmore
★ 3.4k
2
votes
1
reply
7.8k
views
Answer:
A: SRX from SRR IDs
7.0 years ago by
James Ashmore
★ 3.4k
1
vote
0
replies
6.8k
views
Answer:
A: Blacklisted regions for mm10
7.0 years ago by
James Ashmore
★ 3.4k
0
votes
1
reply
2.5k
views
Answer:
A: Looking for wig base coverage file for hg19
7.0 years ago by
James Ashmore
★ 3.4k
2
votes
1
reply
12k
views
Answer:
A: MACS2 with multiple replicates
7.1 years ago by
James Ashmore
★ 3.4k
0
votes
2
replies
2.4k
views
Answer:
A: number of MAPQ=0 reads or alignments in BWA MEM output
7.1 years ago by
James Ashmore
★ 3.4k
1
vote
0
replies
4.1k
views
Answer:
A: Trim FASTA header in multifasta file
7.1 years ago by
James Ashmore
★ 3.4k
2
votes
1
reply
1.5k
views
Answer:
A: Divide each fasta sequence into fragments of 200 nucleotides
7.1 years ago by
James Ashmore
★ 3.4k
2
votes
2
replies
7.8k
views
Answer:
A: FastQC in R
7.1 years ago by
James Ashmore
★ 3.4k
2
votes
0
replies
25k
views
Answer:
A: PC3 & PC2 using plotPCA function in R
7.1 years ago by
James Ashmore
★ 3.4k
4
votes
1
reply
1.6k
views
Answer:
A: Binning the genomic regions and counting reads
7.1 years ago by
James Ashmore
★ 3.4k
0
votes
0
replies
11k
views
Answer:
A: How to calculate RPKM from featureCounts output
7.2 years ago by
James Ashmore
★ 3.4k
16
votes
4
replies
25k
views
Answer:
Answer: Run multiple fastq.gz files with FastQC and yield single report?
updated 19 months ago by
Ram
43k • written 8.8 years ago by
James Ashmore
★ 3.4k
21
votes
1
reply
4.1k
views
Answer:
A: Do I have to check every fastqc to make good quality?
7.9 years ago by
James Ashmore
★ 3.4k
1
vote
0
replies
2.3k
views
Answer:
A: For Chip-seq, which control data I should choose for each biological replicate s
7.9 years ago by
James Ashmore
★ 3.4k
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