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711
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Comment: Comment: Why don't I see people calculating FPKM from normalized read counts?
9 days ago by kalavattam ▴ 350
2
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711
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Comment: Comment: Why don't I see people calculating FPKM from normalized read counts?
9 days ago by kalavattam ▴ 350
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308
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Comment: Comment: Changing order of elements on Chord diagram in R
7 weeks ago by kalavattam ▴ 350
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0
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614
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Comment: Comment: Correct format for Hi-C matrix before converting to BEDPE
7 weeks ago by kalavattam ▴ 350
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0
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202
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Conventions for designing flowcharts for bioinformatics workflows
workflow flowchart diagram pipeline
updated 7 weeks ago by 45k • written 8 weeks ago by ▴ 350
0
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1
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614
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Comment: Comment: Correct format for Hi-C matrix before converting to BEDPE
8 weeks ago by kalavattam ▴ 350
0
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1
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614
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Answer: Answer: Correct format for Hi-C matrix before converting to BEDPE
8 weeks ago by kalavattam ▴ 350
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0
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1.3k
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Comment: Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
10 weeks ago by kalavattam ▴ 350
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1
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1.3k
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Comment: Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
10 weeks ago by kalavattam ▴ 350
0
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0
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1.3k
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Comment: Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
10 weeks ago by kalavattam ▴ 350
5
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9
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1.3k
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Preventing Conda/Mamba from accessing Anaconda repos when institution blocks them
conda mamba repos miniforge channels
updated 10 weeks ago by ▴ 870 • written 10 weeks ago by ▴ 350
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1
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1.3k
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Comment: Comment: Preventing Conda/Mamba from accessing Anaconda repos when institution blocks the
10 weeks ago by kalavattam ▴ 350
0
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0
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490
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Answer: Answer: ChIP-Seq
12 weeks ago by kalavattam ▴ 350
1
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0
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459
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Comment: Comment: Hi-C interactions significance
12 weeks ago by kalavattam ▴ 350
2
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0
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492
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Answer: Answer: Hi-C Pro
12 weeks ago by kalavattam ▴ 350
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0
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1.2k
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Comment: Comment: Estimating effective genome size when retaining a higher-confidence subset of mu
12 weeks ago by kalavattam ▴ 350
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2
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1.2k
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Comment: Comment: Estimating effective genome size when retaining a higher-confidence subset of mu
12 weeks ago by kalavattam ▴ 350
0
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0
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384
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Answer: Answer: merging .cool files of replicates
12 weeks ago by kalavattam ▴ 350
0
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4
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1.2k
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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 12 weeks ago by 151k • written 12 weeks ago by ▴ 350
1
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1
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911
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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
3 months ago by kalavattam ▴ 350
1
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0
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911
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Answer: Answer: On applying spike-in-derived scaling factors to ChIP-seq data: adjust for backgr
3 months ago by kalavattam ▴ 350
1
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1
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1.7k
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Comment: Comment: Is a SLURM job array submission suitable for parallelizing multiple FASTQ file d
5 months ago by kalavattam ▴ 350
9
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12
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1.7k
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Is a SLURM job array submission suitable for parallelizing multiple FASTQ file downloads?
parallel-computing HPC SLURM FASTQ
updated 5 months ago by ★ 2.1k • written 5 months ago by ▴ 350
0
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0
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512
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Comment: Comment: Bos Taurus, Bos Indicus and Bubalus bubalis GTF,GFF,GFF3 file
6 months ago by kalavattam ▴ 350
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0
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512
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Comment: Comment: Bos Taurus, Bos Indicus and Bubalus bubalis GTF,GFF,GFF3 file
6 months ago by kalavattam ▴ 350
0
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0
replies
978
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Answer: Answer: remove the letter a from a biplot in ggplot
7 months ago by kalavattam ▴ 350
0
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0
replies
522
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Adjusting MACS3 --slocal and --llocal parameters for small-genome organisms like S. cerevisiae?
yeast poisson ChIP-seq macs3 peak-calling
7 months ago by kalavattam ▴ 350
1
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1
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624
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Seeking advice on methods to calculate ENCODE ChIP-seq data standard M_DISTINCT
ChIP-seq quality-check ENCODE library-complexity
7 months ago by kalavattam ▴ 350
1
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0
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624
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Answer: Answer: Seeking advice on methods to calculate ENCODE ChIP-seq data standard M_DISTINCT
7 months ago by kalavattam ▴ 350
0
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0
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4.2k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
8 months ago by kalavattam ▴ 350
0
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0
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950
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Comment: Comment: Low "assigned alignments" in output and high "Unassigned_NoFeatures" in summary
9 months ago by kalavattam ▴ 350
2
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1
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973
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Comment: Comment: What should be the term, "insert" or "insert size"?
9 months ago by kalavattam ▴ 350
1
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0
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798
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Answer: Answer: Does single-end short-read sequencing affect the mapping of mitochondrial and ri
9 months ago by kalavattam ▴ 350
0
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0
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3.6k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
9 months ago by kalavattam ▴ 350
0
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2
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3.6k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
9 months ago by kalavattam ▴ 350
0
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1
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3.6k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
9 months ago by kalavattam ▴ 350
0
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1
reply
3.6k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
9 months ago by kalavattam ▴ 350
0
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1
reply
3.6k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
9 months ago by kalavattam ▴ 350
0
votes
1
reply
3.6k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
9 months ago by kalavattam ▴ 350
0
votes
1
reply
3.6k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
9 months ago by kalavattam ▴ 350
0
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1
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3.6k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
9 months ago by kalavattam ▴ 350
3
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2
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3.6k
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Answer: Answer: How can I convert multiple bam files in a directory into fastq files using samt
9 months ago by kalavattam ▴ 350
0
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0
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3.5k
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Answer: Answer: Reheadering a subsetted bam gives truncated file
9 months ago by kalavattam ▴ 350
1
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1
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1.1k
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Comment: Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
9 months ago by kalavattam ▴ 350
1
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1
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1.1k
views
Comment: Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
10 months ago by kalavattam ▴ 350
1
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3
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1.3k
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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
11 months ago by kalavattam ▴ 350
1
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0
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1.3k
views
Answer: Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
11 months ago by kalavattam ▴ 350
0
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0
replies
1.3k
views
Comment: Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
11 months ago by kalavattam ▴ 350
0
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0
replies
437
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Seeking blacklist (exclusion list) for S. cerevisiae in ChIP-seq analysis
QC blacklist ChIP-seq
15 months ago by kalavattam ▴ 350
2
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1
reply
622
views
Optimal MACS2/3 configuration for paired-end ChIP-seq data: `-f BAM` versus `-f BAMPE`
MACS3 peak-calling MACS2 ChIP-seq
updated 15 months ago by 87k • written 15 months ago by ▴ 350
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