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Comment: Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
16 months ago by kalavattam ▴ 380
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603
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Seeking blacklist (exclusion list) for S. cerevisiae in ChIP-seq analysis
QC blacklist ChIP-seq
20 months ago by kalavattam ▴ 380
2
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1
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849
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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 20 months ago by 89k • written 20 months ago by ▴ 380
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21k
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Comment: Comment: BEDOPS gtf2bed conversion error with Ensembl GTF
23 months ago by kalavattam ▴ 380
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2.3k
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Comment: Comment: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
23 months ago by kalavattam ▴ 380
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2.5k
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Comment: Comment: How to convert data in r?
24 months ago by kalavattam ▴ 380
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1
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2.5k
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Comment: Comment: How to convert data in r?
24 months ago by kalavattam ▴ 380
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4.9k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
2.0 years ago by kalavattam ▴ 380
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1
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4.9k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
2.0 years ago by kalavattam ▴ 380
0
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1
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2.3k
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Answer: Answer: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
2.0 years ago by kalavattam ▴ 380
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2.9k
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Comment: Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
2.0 years ago by kalavattam ▴ 380
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2
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2.9k
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Comment: Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
updated 2.0 years ago by 45k • written 2.1 years ago by ▴ 380
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1
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1.3k
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Comment: Comment: Centrality analysis to identify TFs
2.1 years ago by kalavattam ▴ 380
6
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5
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2.9k
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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 2.0 years ago by 45k • written 2.1 years ago by ▴ 380
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2.6k
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Answer: Answer: What is an appropriate cut off for p-values and log fold changes during the anal
2.1 years ago by kalavattam ▴ 380
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1
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4.9k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
2.1 years ago by kalavattam ▴ 380
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0
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4.9k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
2.1 years ago by kalavattam ▴ 380
0
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1
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4.9k
views
Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
2.1 years ago by kalavattam ▴ 380
0
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1
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4.9k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
2.1 years ago by kalavattam ▴ 380
10
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13
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4.9k
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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 months ago by kalavattam ▴ 380
1
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1
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1.5k
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Spike-in normalization via deepTools multiBamSummary --scalingFactors: What's an appropriate --binSize?
spike-in ChIP-seq deepTools
updated 2.1 years ago by ★ 1.6k • written 2.1 years ago by ▴ 380
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267k
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Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
2.1 years ago by kalavattam ▴ 380
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0
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267k
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Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
2.1 years ago by kalavattam ▴ 380
2
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1
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2.7k
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Comment: Comment: new visualization method for dimension reduction technique
2.2 years ago by kalavattam ▴ 380
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0
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2.4k
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Comment: Comment: bowtie2 mapping qualities of 0
2.2 years ago by kalavattam ▴ 380
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0
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2.3k
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Comment: Comment: Dealing with multimapped reads with Chip-seq and ATAC-seq data when studying Tra
2.2 years ago by kalavattam ▴ 380
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0
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3.5k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
2.3 years ago by kalavattam ▴ 380
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0
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3.5k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
2.3 years ago by kalavattam ▴ 380
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0
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3.5k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
2.3 years ago by kalavattam ▴ 380
0
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1
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3.5k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
2.3 years ago by kalavattam ▴ 380
0
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1
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3.5k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
2.3 years ago by kalavattam ▴ 380
6
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17
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3.5k
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MacOS Quicklook plugin for gtf and gff3 files?
gtf gff3 MacOS
updated 2.3 years ago by 45k • written 2.3 years ago by ▴ 380
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3.5k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
2.3 years ago by kalavattam ▴ 380
0
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1
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3.5k
views
Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
2.3 years ago by kalavattam ▴ 380
0
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1
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3.5k
views
Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
2.3 years ago by kalavattam ▴ 380
0
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0
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2.5k
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Comment: Comment: On "wings" in volcano plots...
2.3 years ago by kalavattam ▴ 380
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3
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2.5k
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Comment: Comment: On "wings" in volcano plots...
2.3 years ago by kalavattam ▴ 380
7
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6
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2.5k
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On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 2.3 years ago by 89k • written 2.3 years ago by ▴ 380
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0
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1.5k
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Comment: Comment: How much resources does HiCanu need to assemble PacBio sequence
2.4 years ago by kalavattam ▴ 380
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0
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34k
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Comment: Comment: Bowtie2 parameters for best alignment
2.5 years ago by kalavattam ▴ 380
1
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0
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585
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Split RNA-seq bam by strand: normalize before or after split?
strand forward RNA-seq bam reverse
2.9 years ago by kalavattam ▴ 380
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0
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4.1k
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Answer: Answer: Merge STAR Log.final.out files together
3.2 years ago by kalavattam ▴ 380
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1
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2.2k
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Comment: Comment: Mapping reads using kallisto - rna seq analysis
3.2 years ago by kalavattam ▴ 380
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0
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1.4k
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Comment: Comment: Reference Annotation GTF that includes piRNAs?
3.2 years ago by kalavattam ▴ 380
0
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1
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1.4k
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Comment: Comment: Reference Annotation GTF that includes piRNAs?
3.2 years ago by kalavattam ▴ 380
0
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1
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2.2k
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Comment: Comment: Mapping reads using kallisto - rna seq analysis
3.2 years ago by kalavattam ▴ 380
0
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0
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2.1k
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Comment: Comment: Quick way to get a field such as QNAME from the last read in a bam file?
2.1 years ago by kalavattam ▴ 380
0
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1
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2.1k
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Comment: Comment: Quick way to get a field such as QNAME from the last read in a bam file?
3.2 years ago by kalavattam ▴ 380
0
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1
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2.1k
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Comment: Comment: Quick way to get a field such as QNAME from the last read in a bam file?
3.2 years ago by kalavattam ▴ 380
2
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6
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2.1k
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Quick way to get a field such as QNAME from the last read in a bam file?
bam samtools
2.1 years ago by kalavattam ▴ 380
117 results • Page 2 of 3
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