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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
updated 1 day ago by 14k • written 1 day ago by ▴ 190
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175
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Seeking blacklist (exclusion list) for S. cerevisiae in ChIP-seq analysis
QC blacklist ChIP-seq
3 months ago by kalavattam ▴ 190
2
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1
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260
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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 3 months ago by 82k • written 3 months ago by ▴ 190
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18k
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Comment: Comment: BEDOPS gtf2bed conversion error with Ensembl GTF
6 months ago by kalavattam ▴ 190
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1.1k
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Comment: Comment: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
6 months ago by kalavattam ▴ 190
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1.4k
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Comment: Comment: How to convert data in r?
7 months ago by kalavattam ▴ 190
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1.4k
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Comment: Comment: How to convert data in r?
7 months ago by kalavattam ▴ 190
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2.3k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
7 months ago by kalavattam ▴ 190
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1
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2.3k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
7 months ago by kalavattam ▴ 190
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1
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1.1k
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Answer: Answer: Is there a way to subsample Hi-C at Hi-C matrix .cool file?
8 months ago by kalavattam ▴ 190
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1.4k
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Comment: Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
8 months ago by kalavattam ▴ 190
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2
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1.4k
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Comment: Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
updated 8 months ago by 43k • written 8 months ago by ▴ 190
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693
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Comment: Comment: Centrality analysis to identify TFs
8 months ago by kalavattam ▴ 190
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5
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1.4k
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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 8 months ago by 43k • written 8 months ago by ▴ 190
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1.2k
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Answer: Answer: What is an appropriate cut off for p-values and log fold changes during the anal
8 months ago by kalavattam ▴ 190
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1
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2.3k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
8 months ago by kalavattam ▴ 190
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2.3k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
8 months ago by kalavattam ▴ 190
0
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1
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2.3k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
8 months ago by kalavattam ▴ 190
0
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1
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2.3k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
8 months ago by kalavattam ▴ 190
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11
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2.3k
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Seeking feedback on ChIP-seq normalization method: Calculating scaling factors by dividing input by IP, including spike-in
coverage spike-in scaling-factor ChIP-seq
7 months ago by kalavattam ▴ 190
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656
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Spike-in normalization via deepTools multiBamSummary --scalingFactors: What's an appropriate --binSize?
spike-in ChIP-seq deepTools
updated 8 months ago by ▴ 900 • written 8 months ago by ▴ 190
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240k
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Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
9 months ago by kalavattam ▴ 190
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0
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240k
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Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
9 months ago by kalavattam ▴ 190
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1
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1.0k
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Comment: Comment: new visualization method for dimension reduction technique
9 months ago by kalavattam ▴ 190
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1.3k
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Comment: Comment: bowtie2 mapping qualities of 0
9 months ago by kalavattam ▴ 190
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0
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1.6k
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Comment: Comment: Dealing with multimapped reads with Chip-seq and ATAC-seq data when studying Tra
9 months ago by kalavattam ▴ 190
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0
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1.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
11 months ago by kalavattam ▴ 190
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0
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1.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
11 months ago by kalavattam ▴ 190
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0
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1.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
11 months ago by kalavattam ▴ 190
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1
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1.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
11 months ago by kalavattam ▴ 190
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1
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1.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
11 months ago by kalavattam ▴ 190
6
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17
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1.6k
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MacOS Quicklook plugin for gtf and gff3 files?
gtf gff3 MacOS
updated 11 months ago by 43k • written 11 months ago by ▴ 190
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1.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
11 months ago by kalavattam ▴ 190
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1
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1.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
11 months ago by kalavattam ▴ 190
0
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1
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1.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
11 months ago by kalavattam ▴ 190
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1.4k
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Comment: Comment: On "wings" in volcano plots...
11 months ago by kalavattam ▴ 190
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3
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1.4k
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Comment: Comment: On "wings" in volcano plots...
11 months ago by kalavattam ▴ 190
7
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6
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1.4k
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On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 11 months ago by 82k • written 11 months ago by ▴ 190
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893
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Comment: Comment: How much resources does HiCanu need to assemble PacBio sequence
12 months ago by kalavattam ▴ 190
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0
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29k
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Comment: Comment: Bowtie2 parameters for best alignment
13 months ago by kalavattam ▴ 190
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341
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Split RNA-seq bam by strand: normalize before or after split?
strand forward RNA-seq bam reverse
18 months ago by kalavattam ▴ 190
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3.1k
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Answer: Answer: Merge STAR Log.final.out files together
21 months ago by kalavattam ▴ 190
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1
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1.4k
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Comment: Comment: Mapping reads using kallisto - rna seq analysis
22 months ago by kalavattam ▴ 190
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0
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877
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Comment: Comment: Reference Annotation GTF that includes piRNAs?
22 months ago by kalavattam ▴ 190
0
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1
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877
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Comment: Comment: Reference Annotation GTF that includes piRNAs?
22 months ago by kalavattam ▴ 190
0
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1
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1.4k
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Comment: Comment: Mapping reads using kallisto - rna seq analysis
22 months ago by kalavattam ▴ 190
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0
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1.3k
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Comment: Comment: Quick way to get a field such as QNAME from the last read in a bam file?
8 months ago by kalavattam ▴ 190
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1
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1.3k
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Comment: Comment: Quick way to get a field such as QNAME from the last read in a bam file?
22 months ago by kalavattam ▴ 190
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1
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1.3k
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Comment: Comment: Quick way to get a field such as QNAME from the last read in a bam file?
22 months ago by kalavattam ▴ 190
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6
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1.3k
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Quick way to get a field such as QNAME from the last read in a bam file?
bam samtools
8 months ago by kalavattam ▴ 190
67 results • Page 1 of 2
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