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Answer: Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful?
25 days ago by kalavattam ▴ 380
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14k
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Comment: Comment: MACS2 --SPMR and --nolambda usage for version 2.1.2
27 days ago by kalavattam ▴ 380
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12k
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Comment: Comment: Asking for source of the figure
28 days ago by kalavattam ▴ 380
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1.3k
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Comment: Comment: Why don't I see people calculating FPKM from normalized read counts?
5 months ago by kalavattam ▴ 380
2
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1.3k
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Comment: Comment: Why don't I see people calculating FPKM from normalized read counts?
5 months ago by kalavattam ▴ 380
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524
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Comment: Comment: Changing order of elements on Chord diagram in R
6 months ago by kalavattam ▴ 380
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1.4k
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Comment: Comment: Correct format for Hi-C matrix before converting to BEDPE
6 months ago by kalavattam ▴ 380
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413
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Conventions for designing flowcharts for bioinformatics workflows
workflow flowchart diagram pipeline
updated 6 months ago by 45k • written 6 months ago by ▴ 380
0
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1.4k
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Comment: Comment: Correct format for Hi-C matrix before converting to BEDPE
6 months ago by kalavattam ▴ 380
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1
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1.4k
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Answer: Answer: Correct format for Hi-C matrix before converting to BEDPE
6 months ago by kalavattam ▴ 380
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3.7k
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Comment: Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
7 months ago by kalavattam ▴ 380
0
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1
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3.7k
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Comment: Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
7 months ago by kalavattam ▴ 380
0
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0
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3.7k
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Comment: Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
7 months ago by kalavattam ▴ 380
5
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9
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3.7k
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Preventing Conda/Mamba from accessing Anaconda repos when institution blocks them
conda mamba repos miniforge channels
updated 7 months ago by ▴ 880 • written 7 months ago by ▴ 380
0
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3.7k
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Comment: Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
7 months ago by kalavattam ▴ 380
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0
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884
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Answer: Answer: ChIP-Seq
7 months ago by kalavattam ▴ 380
1
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772
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Comment: Comment: Hi-C interactions significance
7 months ago by kalavattam ▴ 380
2
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784
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Answer: Answer: Hi-C Pro
7 months ago by kalavattam ▴ 380
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1.6k
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Comment: Comment: Estimating effective genome size when retaining a higher-confidence subset of mu
7 months ago by kalavattam ▴ 380
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2
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1.6k
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Comment: Comment: Estimating effective genome size when retaining a higher-confidence subset of mu
7 months ago by kalavattam ▴ 380
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654
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Answer: Answer: merging .cool files of replicates
7 months ago by kalavattam ▴ 380
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4
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1.6k
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Estimating effective genome size when retaining a higher-confidence subset of multi-mappers in alignment data
multi-mapper effective-genome-size complexity mapq
updated 7 months ago by 153k • written 7 months ago by ▴ 380
1
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1
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1.2k
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On applying spike-in-derived scaling factors to ChIP-seq data: adjust for background signal (input) or not?
spike-in deepTools normalization ChIP-seq scaling-factor
7 months ago by kalavattam ▴ 380
1
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1.2k
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Answer: Answer: On applying spike-in-derived scaling factors to ChIP-seq data: adjust for backgr
7 months ago by kalavattam ▴ 380
1
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1
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2.6k
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Comment: Comment: Is a SLURM job array submission suitable for parallelizing multiple FASTQ file d
10 months ago by kalavattam ▴ 380
9
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12
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2.6k
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Is a SLURM job array submission suitable for parallelizing multiple FASTQ file downloads?
parallel-computing HPC SLURM FASTQ
updated 10 months ago by ★ 2.2k • written 10 months ago by ▴ 380
0
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783
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Comment: Comment: Bos Taurus, Bos Indicus and Bubalus bubalis GTF,GFF,GFF3 file
11 months ago by kalavattam ▴ 380
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0
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783
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Comment: Comment: Bos Taurus, Bos Indicus and Bubalus bubalis GTF,GFF,GFF3 file
11 months ago by kalavattam ▴ 380
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1.5k
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Answer: Answer: remove the letter a from a biplot in ggplot
12 months ago by kalavattam ▴ 380
0
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0
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742
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Adjusting MACS3 --slocal and --llocal parameters for small-genome organisms like S. cerevisiae?
yeast poisson ChIP-seq macs3 peak-calling
12 months ago by kalavattam ▴ 380
1
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1
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952
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Seeking advice on methods to calculate ENCODE ChIP-seq data standard M_DISTINCT
ChIP-seq quality-check ENCODE library-complexity
12 months ago by kalavattam ▴ 380
1
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952
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Answer: Answer: Seeking advice on methods to calculate ENCODE ChIP-seq data standard M_DISTINCT
12 months ago by kalavattam ▴ 380
0
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4.9k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
13 months ago by kalavattam ▴ 380
0
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0
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1.4k
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Comment: Comment: Low "assigned alignments" in output and high "Unassigned_NoFeatures" in summary
14 months ago by kalavattam ▴ 380
2
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1
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1.4k
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Comment: Comment: What should be the term, "insert" or "insert size"?
14 months ago by kalavattam ▴ 380
1
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1.2k
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Answer: Answer: Does single-end short-read sequencing affect the mapping of mitochondrial and ri
14 months ago by kalavattam ▴ 380
0
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0
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4.8k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
14 months ago by kalavattam ▴ 380
0
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2
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4.8k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
14 months ago by kalavattam ▴ 380
0
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1
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4.8k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
14 months ago by kalavattam ▴ 380
0
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1
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4.8k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
14 months ago by kalavattam ▴ 380
0
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1
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4.8k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
14 months ago by kalavattam ▴ 380
0
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1
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4.8k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
14 months ago by kalavattam ▴ 380
0
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1
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4.8k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
14 months ago by kalavattam ▴ 380
0
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1
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4.8k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
14 months ago by kalavattam ▴ 380
3
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2
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4.8k
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Answer: Answer: How can I convert multiple bam files in a directory into fastq files using samt
14 months ago by kalavattam ▴ 380
0
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0
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4.0k
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Answer: Answer: Reheadering a subsetted bam gives truncated file
14 months ago by kalavattam ▴ 380
1
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1
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1.4k
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Comment: Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
14 months ago by kalavattam ▴ 380
1
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1
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1.4k
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Comment: Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
14 months ago by kalavattam ▴ 380
1
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3
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1.9k
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Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE BAM SAM flag paired-end
16 months ago by kalavattam ▴ 380
1
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0
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1.9k
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Answer: Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
16 months ago by kalavattam ▴ 380
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