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Comment:
Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
19 days ago by
kalavattam
▴ 270
0
votes
0
replies
185
views
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
0
votes
0
replies
433
views
Comment:
Comment: Low "assigned alignments" in output and high "Unassigned_NoFeatures" in summary
5 weeks ago by
kalavattam
▴ 270
2
votes
1
reply
462
views
Comment:
Comment: What should be the term, "insert" or "insert size"?
5 weeks ago by
kalavattam
▴ 270
1
vote
0
replies
455
views
Answer:
Answer: Does single-end short-read sequencing affect the mapping of mitochondrial and ri
7 weeks ago by
kalavattam
▴ 270
0
votes
0
replies
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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2
replies
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
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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
votes
1
reply
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
votes
1
reply
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
votes
1
reply
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
3
votes
2
replies
1.4k
views
Answer:
Answer: How can I convert multiple bam files in a directory into fastq files using samt
7 weeks ago by
kalavattam
▴ 270
0
votes
0
replies
2.9k
views
Answer:
Answer: Reheadering a subsetted bam gives truncated file
7 weeks ago by
kalavattam
▴ 270
1
vote
1
reply
462
views
Comment:
Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
8 weeks ago by
kalavattam
▴ 270
1
vote
1
reply
462
views
Comment:
Comment: What is the difference between Enrichr and ShinyGO? Which one is the best?
8 weeks ago by
kalavattam
▴ 270
1
vote
3
replies
671
views
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
vote
0
replies
671
views
Answer:
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
3 months ago by
kalavattam
▴ 270
0
votes
0
replies
671
views
Comment:
Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
3 months ago by
kalavattam
▴ 270
0
votes
0
replies
246
views
Seeking blacklist (exclusion list) for S. cerevisiae in ChIP-seq analysis
QC
blacklist
ChIP-seq
7 months ago by
kalavattam
▴ 270
2
votes
1
reply
368
views
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
ATpoint
84k • written 7 months ago by
kalavattam
▴ 270
0
votes
0
replies
19k
views
Comment:
Comment: BEDOPS gtf2bed conversion error with Ensembl GTF
10 months ago by
kalavattam
▴ 270
0
votes
0
replies
1.4k
views
Comment:
Comment: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
10 months ago by
kalavattam
▴ 270
0
votes
1
reply
1.6k
views
Comment:
Comment: How to convert data in r?
11 months ago by
kalavattam
▴ 270
1
vote
1
reply
1.6k
views
Comment:
Comment: How to convert data in r?
11 months ago by
kalavattam
▴ 270
0
votes
0
replies
3.0k
views
Comment:
Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
11 months ago by
kalavattam
▴ 270
0
votes
1
reply
3.0k
views
Comment:
Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
11 months ago by
kalavattam
▴ 270
0
votes
1
reply
1.4k
views
Answer:
Answer: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
12 months ago by
kalavattam
▴ 270
0
votes
0
replies
1.7k
views
Comment:
Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
12 months ago by
kalavattam
▴ 270
0
votes
2
replies
1.7k
views
Comment:
Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
updated 12 months ago by
Ram
44k • written 12 months ago by
kalavattam
▴ 270
0
votes
1
reply
839
views
Comment:
Comment: Centrality analysis to identify TFs
12 months ago by
kalavattam
▴ 270
6
votes
5
replies
1.7k
views
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
Ram
44k • written 12 months ago by
kalavattam
▴ 270
0
votes
0
replies
1.6k
views
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
votes
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
votes
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
votes
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
votes
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
votes
13
replies
3.0k
views
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
vote
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
rfran010
★ 1.3k • written 12 months ago by
kalavattam
▴ 270
0
votes
0
replies
247k
views
Comment:
Comment: Tools To Calculate Average Coverage For A Bam File?
13 months ago by
kalavattam
▴ 270
0
votes
0
replies
247k
views
Comment:
Comment: Tools To Calculate Average Coverage For A Bam File?
13 months ago by
kalavattam
▴ 270
2
votes
1
reply
1.3k
views
Comment:
Comment: new visualization method for dimension reduction technique
13 months ago by
kalavattam
▴ 270
0
votes
0
replies
1.6k
views
Comment:
Comment: bowtie2 mapping qualities of 0
13 months ago by
kalavattam
▴ 270
0
votes
0
replies
1.8k
views
Comment:
Comment: Dealing with multimapped reads with Chip-seq and ATAC-seq data when studying Tra
13 months ago by
kalavattam
▴ 270
0
votes
0
replies
2.0k
views
Comment:
Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by
kalavattam
▴ 270
0
votes
0
replies
2.0k
views
Comment:
Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by
kalavattam
▴ 270
0
votes
0
replies
2.0k
views
Comment:
Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by
kalavattam
▴ 270
0
votes
1
reply
2.0k
views
Comment:
Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by
kalavattam
▴ 270
0
votes
1
reply
2.0k
views
Comment:
Comment: MacOS Quicklook plugin for gtf and gff3 files?
15 months ago by
kalavattam
▴ 270
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