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1
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3
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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
12 days ago by kalavattam ▴ 190
0
votes
0
replies
194
views
Seeking blacklist (exclusion list) for S. cerevisiae in ChIP-seq analysis
QC blacklist ChIP-seq
3 months ago by kalavattam ▴ 190
2
votes
1
reply
288
views
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
6
votes
5
replies
1.5k
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 8 months ago by 44k • written 8 months ago by ▴ 190
10
votes
11
replies
2.4k
views
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
8 months ago by kalavattam ▴ 190
1
vote
1
reply
692
views
Spike-in normalization via deepTools multiBamSummary --scalingFactors: What's an appropriate --binSize?
spike-in ChIP-seq deepTools
updated 9 months ago by ▴ 900 • written 9 months ago by ▴ 190
6
votes
17
replies
1.7k
views
MacOS Quicklook plugin for gtf and gff3 files?
gtf gff3 MacOS
updated 12 months ago by 44k • written 12 months ago by ▴ 190
7
votes
6
replies
1.4k
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 12 months ago by 82k • written 12 months ago by ▴ 190
1
vote
0
replies
351
views
Split RNA-seq bam by strand: normalize before or after split?
strand forward RNA-seq bam reverse
19 months ago by kalavattam ▴ 190
2
votes
6
replies
1.4k
views
Quick way to get a field such as QNAME from the last read in a bam file?
bam samtools
9 months ago by kalavattam ▴ 190
1
vote
1
reply
870
views
Fast way to sort bam file by queryname similar to picard SortSam SORT_ORDER=queryname?
picard samtools bam
updated 11 months ago by 44k • written 23 months ago by ▴ 190
1
vote
4
replies
2.2k
views
Duplicate reads remain in bam after picard MarkDuplicates --REMOVE_DUPLICATES true
deduplication qname fastq Picard bam
2.2 years ago by kalavattam ▴ 190
0
votes
0
replies
590
views
Align sample to two different assemblies, then classify pairs that differ significantly in alignment score
Bowtie2 classification mismatch alignment gaps
2.6 years ago by kalavattam ▴ 190
0
votes
0
replies
585
views
Plot only the genome-wide trans contacts in a Hi-C matrix (no cis contacts)
juicer Hi-C inter-chromosomal cooler trans
3.1 years ago by kalavattam ▴ 190
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