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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
5 days ago by kalavattam ▴ 280
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1
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1.2k
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Comment: Comment: Is a SLURM job array submission suitable for parallelizing multiple FASTQ file d
5 weeks ago by kalavattam ▴ 280
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12
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1.2k
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Is a SLURM job array submission suitable for parallelizing multiple FASTQ file downloads?
parallel-computing HPC SLURM FASTQ
updated 4 weeks ago by ★ 2.1k • written 5 weeks ago by ▴ 280
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353
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Comment: Comment: Bos Taurus, Bos Indicus and Bubalus bubalis GTF,GFF,GFF3 file
9 weeks ago by kalavattam ▴ 280
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353
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Comment: Comment: Bos Taurus, Bos Indicus and Bubalus bubalis GTF,GFF,GFF3 file
9 weeks ago by kalavattam ▴ 280
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470
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Answer: Answer: remove the letter a from a biplot in ggplot
3 months ago by kalavattam ▴ 280
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352
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Adjusting MACS3 --slocal and --llocal parameters for small-genome organisms like S. cerevisiae?
yeast poisson ChIP-seq macs3 peak-calling
3 months ago by kalavattam ▴ 280
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1
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419
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Seeking advice on methods to calculate ENCODE ChIP-seq data standard M_DISTINCT
ChIP-seq quality-check ENCODE library-complexity
3 months ago by kalavattam ▴ 280
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0
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419
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Answer: Answer: Seeking advice on methods to calculate ENCODE ChIP-seq data standard M_DISTINCT
3 months ago by kalavattam ▴ 280
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0
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3.4k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
4 months ago by kalavattam ▴ 280
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0
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559
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Comment: Comment: Low "assigned alignments" in output and high "Unassigned_NoFeatures" in summary
4 months ago by kalavattam ▴ 280
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1
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594
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Comment: Comment: What should be the term, "insert" or "insert size"?
4 months ago by kalavattam ▴ 280
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0
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525
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Answer: Answer: Does single-end short-read sequencing affect the mapping of mitochondrial and ri
5 months ago by kalavattam ▴ 280
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0
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1.9k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
5 months ago by kalavattam ▴ 280
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2
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1.9k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
5 months ago by kalavattam ▴ 280
0
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1
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1.9k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
5 months ago by kalavattam ▴ 280
0
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1
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1.9k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
5 months ago by kalavattam ▴ 280
0
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1
reply
1.9k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
5 months ago by kalavattam ▴ 280
0
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1
reply
1.9k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
5 months ago by kalavattam ▴ 280
0
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1
reply
1.9k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
5 months ago by kalavattam ▴ 280
0
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1
reply
1.9k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
5 months ago by kalavattam ▴ 280
3
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2
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1.9k
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Answer: Answer: How can I convert multiple bam files in a directory into fastq files using samt
5 months ago by kalavattam ▴ 280
0
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0
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3.0k
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Answer: Answer: Reheadering a subsetted bam gives truncated file
5 months ago by kalavattam ▴ 280
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1
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654
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Comment: Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
5 months ago by kalavattam ▴ 280
1
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1
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654
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Comment: Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
5 months ago by kalavattam ▴ 280
1
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3
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895
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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
7 months ago by kalavattam ▴ 280
1
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0
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895
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Answer: Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
7 months ago by kalavattam ▴ 280
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0
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895
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Comment: Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
7 months ago by kalavattam ▴ 280
0
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0
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316
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Seeking blacklist (exclusion list) for S. cerevisiae in ChIP-seq analysis
QC blacklist ChIP-seq
10 months ago by kalavattam ▴ 280
2
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1
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453
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Optimal MACS2/3 configuration for paired-end ChIP-seq data: `-f BAM` versus `-f BAMPE`
MACS3 peak-calling MACS2 ChIP-seq
updated 10 months ago by 86k • written 10 months ago by ▴ 280
0
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0
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19k
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Comment: Comment: BEDOPS gtf2bed conversion error with Ensembl GTF
13 months ago by kalavattam ▴ 280
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0
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1.5k
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Comment: Comment: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
14 months ago by kalavattam ▴ 280
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1
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1.7k
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Comment: Comment: How to convert data in r?
14 months ago by kalavattam ▴ 280
1
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1
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1.7k
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Comment: Comment: How to convert data in r?
14 months ago by kalavattam ▴ 280
0
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0
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3.4k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
15 months ago by kalavattam ▴ 280
0
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1
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3.4k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
15 months ago by kalavattam ▴ 280
0
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1
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1.5k
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Answer: Answer: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
15 months ago by kalavattam ▴ 280
0
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0
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2.0k
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Comment: Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
15 months ago by kalavattam ▴ 280
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2
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2.0k
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Comment: Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
updated 15 months ago by 44k • written 15 months ago by ▴ 280
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1
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929
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Comment: Comment: Centrality analysis to identify TFs
15 months ago by kalavattam ▴ 280
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5
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2.0k
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ChIP-seq visualization: Is it valid to do a coverage normalization in addition to applying a spike-in-derived scaling factor?
ChIP-seq normalization scaling-factor coverage spike-in
updated 15 months ago by 44k • written 15 months ago by ▴ 280
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0
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1.8k
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Answer: Answer: What is an appropriate cut off for p-values and log fold changes during the anal
15 months ago by kalavattam ▴ 280
0
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1
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3.4k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
15 months ago by kalavattam ▴ 280
0
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0
replies
3.4k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
16 months ago by kalavattam ▴ 280
0
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1
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3.4k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
16 months ago by kalavattam ▴ 280
0
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1
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3.4k
views
Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
15 months ago by kalavattam ▴ 280
10
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13
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3.4k
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Seeking feedback on ChIP-seq normalization method: Calculating scaling factors by dividing input by IP, including spike-in
ChIP-seq spike-in scaling-factor coverage
3 months ago by kalavattam ▴ 280
1
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1
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949
views
Spike-in normalization via deepTools multiBamSummary --scalingFactors: What's an appropriate --binSize?
spike-in ChIP-seq deepTools
updated 16 months ago by ★ 1.3k • written 16 months ago by ▴ 280
0
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0
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253k
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Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
16 months ago by kalavattam ▴ 280
0
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0
replies
253k
views
Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
16 months ago by kalavattam ▴ 280
94 results • Page 1 of 2
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