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0
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1
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3.2k
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Comment: C: Bowtie fails to align reads that appear in the reference sequence
8.5 years ago by James Ashmore ★ 3.5k
0
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0
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2.0k
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Comment: C: Binning the genomic regions and counting reads
8.5 years ago by James Ashmore ★ 3.5k
0
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0
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3.3k
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Comment: C: Fast and reproducible method to downsample a count matrix to different sequencin
8.5 years ago by James Ashmore ★ 3.5k
0
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2
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3.3k
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Fast and reproducible method to downsample a count matrix to different sequencing depths?
R
8.5 years ago by James Ashmore ★ 3.5k
0
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0
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2.9k
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Comment: C: Existing software to calculate RNASeq read distribution by "gene_type" (Gencode)
8.5 years ago by James Ashmore ★ 3.5k
2
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0
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27k
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Answer: A: PC3 & PC2 using plotPCA function in R
8.5 years ago by James Ashmore ★ 3.5k
4
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1
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2.0k
views
Answer: A: Binning the genomic regions and counting reads
8.5 years ago by James Ashmore ★ 3.5k
0
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0
replies
4.6k
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Comment: C: Quantile normalization and variability questions
8.5 years ago by James Ashmore ★ 3.5k
2
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1
reply
4.6k
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Comment: C: Quantile normalization and variability questions
8.5 years ago by James Ashmore ★ 3.5k
0
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1
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2.5k
views
Comment: C: fastQC - case of the anomalous last base
8.5 years ago by James Ashmore ★ 3.5k
1
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1
reply
8.0k
views
Comment: C: mitochondrial blacklists ATAC-Seq
8.5 years ago by James Ashmore ★ 3.5k
0
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0
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15k
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Comment: C: Trimmomatic - unknown trimmer?
8.5 years ago by James Ashmore ★ 3.5k
0
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0
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4.8k
views
Comment: C: Different alignments rates with bwa mem (0%) and bowtie2 (82%)
8.6 years ago by James Ashmore ★ 3.5k
0
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4
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4.8k
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Different alignments rates with bwa mem (0%) and bowtie2 (82%)
bwa bowtie2
8.6 years ago by James Ashmore ★ 3.5k
0
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0
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7.6k
views
Comment: C: Removal of repeat and blacklist regions from ChIP-seq data
8.6 years ago by James Ashmore ★ 3.5k
0
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1
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7.6k
views
Comment: C: Removal of repeat and blacklist regions from ChIP-seq data
8.6 years ago by James Ashmore ★ 3.5k
1
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1
reply
7.6k
views
Comment: C: Removal of repeat and blacklist regions from ChIP-seq data
8.6 years ago by James Ashmore ★ 3.5k
0
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0
replies
12k
views
Answer: A: How to calculate RPKM from featureCounts output
8.6 years ago by James Ashmore ★ 3.5k
1
vote
1
reply
203k
views
Comment: C: The Biostar Handbook. A bioinformatics e-book for beginners.
8.8 years ago by James Ashmore ★ 3.5k
0
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0
replies
27k
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Comment: C: Run multiple fastq.gz files with FastQC and yield single report?
8.8 years ago by James Ashmore ★ 3.5k
0
votes
1
reply
3.2k
views
Removing GC content bias and trended bias from ChIP-seq data
csaw ChIP-Seq normalisation edgeR CQN
8.9 years ago by James Ashmore ★ 3.5k
0
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0
replies
1.6k
views
Comment: C: error using the F-seq tool
9.0 years ago by James Ashmore ★ 3.5k
0
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0
replies
2.5k
views
Comment: C: Compromise null hypothesis when calling differential binding between ChIP-seq co
9.1 years ago by James Ashmore ★ 3.5k
16
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4
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27k
views
Answer: Answer: Run multiple fastq.gz files with FastQC and yield single report?
updated 3.0 years ago by 45k • written 10.1 years ago by ★ 3.5k
3
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0
replies
4.9k
views
Comment: C: Using getopt module to parse and define command line arguments in python
9.2 years ago by James Ashmore ★ 3.5k
0
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0
replies
4.8k
views
Comment: C: How to handle metadata in bioinformatics pipelines?
9.3 years ago by James Ashmore ★ 3.5k
11
votes
9
replies
4.8k
views
6 follow
How to handle metadata in bioinformatics pipelines?
metadata pipeline snakemake make
updated 9.3 years ago by 23k • written 9.3 years ago by ★ 3.5k
0
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0
replies
3.6k
views
Comment: C: Quick way to Identify batch effect from covariates?
9.3 years ago by James Ashmore ★ 3.5k
3
votes
3
replies
3.6k
views
Quick way to Identify batch effect from covariates?
bioconductor batch-effect
updated 17 months ago by 45k • written 9.3 years ago by ★ 3.5k
1
vote
1
reply
8.0k
views
Comment: C: Trimmomatic not removing all Nextera adapters or N base calls
9.3 years ago by James Ashmore ★ 3.5k
0
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1
reply
4.1k
views
Comment: C: Bedtools coverage gives zero coverage output
9.3 years ago by James Ashmore ★ 3.5k
0
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1
reply
4.1k
views
Comment: C: Bedtools coverage gives zero coverage output
9.3 years ago by James Ashmore ★ 3.5k
0
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1
reply
4.1k
views
Comment: C: Bedtools coverage gives zero coverage output
9.3 years ago by James Ashmore ★ 3.5k
21
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1
reply
5.5k
views
Answer: A: Do I have to check every fastqc to make good quality?
9.3 years ago by James Ashmore ★ 3.5k
1
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0
replies
2.7k
views
Answer: A: For Chip-seq, which control data I should choose for each biological replicate s
9.3 years ago by James Ashmore ★ 3.5k
3
votes
4
replies
8.0k
views
Trimmomatic not removing all Nextera adapters or N base calls
trimming nextera trimmomatic
updated 9.4 years ago by 20 • written 9.4 years ago by ★ 3.5k
0
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1
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8.0k
views
Comment: C: Trimmomatic not removing all Nextera adapters or N base calls
9.4 years ago by James Ashmore ★ 3.5k
2
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3
replies
5.4k
views
Comment: C: flagstats bam file
9.4 years ago by James Ashmore ★ 3.5k
0
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1
reply
3.4k
views
Comment: C: How would you discover the source of contaminant DNA ?
9.4 years ago by James Ashmore ★ 3.5k
1
vote
0
replies
14k
views
Comment: C: Shifting reads for ATAC-seq alignments
9.4 years ago by James Ashmore ★ 3.5k
5
votes
3
replies
14k
views
Answer: A: Shifting reads for ATAC-seq alignments
9.4 years ago by James Ashmore ★ 3.5k
0
votes
1
reply
11k
views
Comment: C: [Python] How to convert a list to a dictionary if dict() does not work without u
9.4 years ago by James Ashmore ★ 3.5k
2
votes
1
reply
2.6k
views
Comment: C: Any state of the art tool for reads generation from reference sequence?
9.4 years ago by James Ashmore ★ 3.5k
1
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1
reply
3.1k
views
Answer: C: goseq package: cannot find function supportedOrganisms()
9.5 years ago by James Ashmore ★ 3.5k
0
votes
1
reply
3.1k
views
Comment: C: goseq package: cannot find function supportedOrganisms()
9.5 years ago by James Ashmore ★ 3.5k
3
votes
0
replies
7.6k
views
Answer: A: Help, how to read wig files into R?
9.5 years ago by James Ashmore ★ 3.5k
0
votes
1
reply
2.8k
views
Comment: C: Difficulty replicating likelihood ratio test from RNA-seq paper
9.5 years ago by James Ashmore ★ 3.5k
5
votes
3
replies
2.8k
views
Difficulty replicating likelihood ratio test from RNA-seq paper
RNA-Seq R
updated 9.5 years ago by ▴ 1000 • written 9.5 years ago by ★ 3.5k
0
votes
0
replies
8.3k
views
Comment: C: How to remove empty read from fastq
9.5 years ago by James Ashmore ★ 3.5k
0
votes
0
replies
2.3k
views
Comment: C: Resources to understand regression models for count data
9.5 years ago by James Ashmore ★ 3.5k
290 results • Page 4 of 6
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