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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
19 days ago by kalavattam ▴ 270
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185
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Seeking advice on methods to calculate ENCODE ChIP-seq data standard M_DISTINCT
ChIP-seq quality-check ENCODE library-complexity
4 weeks ago by kalavattam ▴ 270
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0
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433
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Comment: Comment: Low "assigned alignments" in output and high "Unassigned_NoFeatures" in summary
5 weeks ago by kalavattam ▴ 270
2
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1
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462
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Comment: Comment: What should be the term, "insert" or "insert size"?
5 weeks ago by kalavattam ▴ 270
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0
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455
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Answer: Answer: Does single-end short-read sequencing affect the mapping of mitochondrial and ri
7 weeks ago by kalavattam ▴ 270
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0
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1.4k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by kalavattam ▴ 270
0
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2
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1.4k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by kalavattam ▴ 270
0
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1
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1.4k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by kalavattam ▴ 270
0
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1
reply
1.4k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by kalavattam ▴ 270
0
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1
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1.4k
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Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by kalavattam ▴ 270
0
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1
reply
1.4k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by kalavattam ▴ 270
0
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1
reply
1.4k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by kalavattam ▴ 270
0
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1
reply
1.4k
views
Comment: Comment: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by kalavattam ▴ 270
3
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2
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1.4k
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Answer: Answer: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by kalavattam ▴ 270
0
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0
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2.9k
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Answer: Answer: Reheadering a subsetted bam gives truncated file
7 weeks ago by kalavattam ▴ 270
1
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1
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462
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Comment: Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
8 weeks ago by kalavattam ▴ 270
1
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1
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462
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Comment: Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
8 weeks ago by kalavattam ▴ 270
1
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3
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671
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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
3 months ago by kalavattam ▴ 270
1
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0
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671
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Answer: Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
3 months ago by kalavattam ▴ 270
0
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0
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671
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Comment: Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
3 months ago by kalavattam ▴ 270
0
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0
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246
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Seeking blacklist (exclusion list) for S. cerevisiae in ChIP-seq analysis
QC blacklist ChIP-seq
7 months ago by kalavattam ▴ 270
2
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1
reply
368
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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 7 months ago by 84k • written 7 months ago by ▴ 270
0
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0
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19k
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Comment: Comment: BEDOPS gtf2bed conversion error with Ensembl GTF
10 months ago by kalavattam ▴ 270
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0
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1.4k
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Comment: Comment: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
10 months ago by kalavattam ▴ 270
0
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1
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1.6k
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Comment: Comment: How to convert data in r?
11 months ago by kalavattam ▴ 270
1
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1
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1.6k
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Comment: Comment: How to convert data in r?
11 months ago by kalavattam ▴ 270
0
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0
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3.0k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
11 months ago by kalavattam ▴ 270
0
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1
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3.0k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
11 months ago by kalavattam ▴ 270
0
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1
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1.4k
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Answer: Answer: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
12 months ago by kalavattam ▴ 270
0
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0
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1.7k
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Comment: Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
12 months ago by kalavattam ▴ 270
0
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2
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1.7k
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Comment: Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
updated 12 months ago by 44k • written 12 months ago by ▴ 270
0
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1
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839
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Comment: Comment: Centrality analysis to identify TFs
12 months ago by kalavattam ▴ 270
6
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5
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1.7k
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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 12 months ago by 44k • written 12 months ago by ▴ 270
0
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0
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1.6k
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Answer: Answer: What is an appropriate cut off for p-values and log fold changes during the anal
12 months ago by kalavattam ▴ 270
0
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1
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3.0k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
12 months ago by kalavattam ▴ 270
0
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0
replies
3.0k
views
Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
12 months ago by kalavattam ▴ 270
0
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1
reply
3.0k
views
Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
12 months ago by kalavattam ▴ 270
0
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1
reply
3.0k
views
Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
12 months ago by kalavattam ▴ 270
10
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13
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3.0k
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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
13 days ago by kalavattam ▴ 270
1
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1
reply
816
views
Spike-in normalization via deepTools multiBamSummary --scalingFactors: What's an appropriate --binSize?
spike-in ChIP-seq deepTools
updated 12 months ago by ★ 1.3k • written 12 months ago by ▴ 270
0
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0
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247k
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Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
13 months ago by kalavattam ▴ 270
0
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0
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247k
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Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
13 months ago by kalavattam ▴ 270
2
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1
reply
1.3k
views
Comment: Comment: new visualization method for dimension reduction technique
13 months ago by kalavattam ▴ 270
0
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0
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1.6k
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Comment: Comment: bowtie2 mapping qualities of 0
13 months ago by kalavattam ▴ 270
0
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0
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1.8k
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Comment: Comment: Dealing with multimapped reads with Chip-seq and ATAC-seq data when studying Tra
13 months ago by kalavattam ▴ 270
0
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0
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2.0k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by kalavattam ▴ 270
0
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0
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2.0k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by kalavattam ▴ 270
0
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0
replies
2.0k
views
Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by kalavattam ▴ 270
0
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1
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2.0k
views
Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by kalavattam ▴ 270
0
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1
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2.0k
views
Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by kalavattam ▴ 270
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