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Comment: Comment: ChIP-seq visualization: Is it valid to do a coverage normalization in addition t
updated 17 months ago by 44k • written 17 months ago by ▴ 310
0
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1
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1.0k
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Comment: Comment: Centrality analysis to identify TFs
17 months ago by kalavattam ▴ 310
6
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5
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2.3k
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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 17 months ago by 44k • written 17 months ago by ▴ 310
0
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0
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2.0k
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Answer: Answer: What is an appropriate cut off for p-values and log fold changes during the anal
18 months ago by kalavattam ▴ 310
0
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1
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3.8k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
18 months ago by kalavattam ▴ 310
0
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0
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3.8k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
18 months ago by kalavattam ▴ 310
0
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1
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3.8k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
18 months ago by kalavattam ▴ 310
0
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1
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3.8k
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Comment: Comment: Seeking feedback on ChIP-seq normalization method: Calculating scaling factors b
18 months ago by kalavattam ▴ 310
10
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13
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3.8k
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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
6 months ago by kalavattam ▴ 310
1
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1
reply
1.1k
views
Spike-in normalization via deepTools multiBamSummary --scalingFactors: What's an appropriate --binSize?
spike-in ChIP-seq deepTools
updated 18 months ago by ★ 1.3k • written 18 months ago by ▴ 310
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0
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256k
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Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
18 months ago by kalavattam ▴ 310
0
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0
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256k
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Comment: Comment: Tools To Calculate Average Coverage For A Bam File?
18 months ago by kalavattam ▴ 310
2
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1
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1.8k
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Comment: Comment: new visualization method for dimension reduction technique
19 months ago by kalavattam ▴ 310
0
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0
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1.9k
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Comment: Comment: bowtie2 mapping qualities of 0
19 months ago by kalavattam ▴ 310
0
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0
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2.0k
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Comment: Comment: Dealing with multimapped reads with Chip-seq and ATAC-seq data when studying Tra
19 months ago by kalavattam ▴ 310
0
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0
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2.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
21 months ago by kalavattam ▴ 310
0
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0
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2.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
21 months ago by kalavattam ▴ 310
0
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0
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2.6k
views
Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
21 months ago by kalavattam ▴ 310
0
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1
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2.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
21 months ago by kalavattam ▴ 310
0
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1
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2.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
21 months ago by kalavattam ▴ 310
6
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17
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2.6k
views
MacOS Quicklook plugin for gtf and gff3 files?
gtf gff3 MacOS
updated 21 months ago by 44k • written 21 months ago by ▴ 310
0
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1
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2.6k
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Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
21 months ago by kalavattam ▴ 310
0
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1
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2.6k
views
Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
21 months ago by kalavattam ▴ 310
0
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1
reply
2.6k
views
Comment: Comment: MacOS Quicklook plugin for gtf and gff3 files?
21 months ago by kalavattam ▴ 310
0
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0
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1.9k
views
Comment: Comment: On "wings" in volcano plots...
21 months ago by kalavattam ▴ 310
0
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3
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1.9k
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Comment: Comment: On "wings" in volcano plots...
21 months ago by kalavattam ▴ 310
7
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6
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1.9k
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On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 21 months ago by 87k • written 21 months ago by ▴ 310
0
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0
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1.2k
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Comment: Comment: How much resources does HiCanu need to assemble PacBio sequence
22 months ago by kalavattam ▴ 310
0
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0
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31k
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Comment: Comment: Bowtie2 parameters for best alignment
23 months ago by kalavattam ▴ 310
1
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0
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493
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Split RNA-seq bam by strand: normalize before or after split?
strand forward RNA-seq bam reverse
2.3 years ago by kalavattam ▴ 310
0
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0
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3.6k
views
Answer: Answer: Merge STAR Log.final.out files together
2.6 years ago by kalavattam ▴ 310
0
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1
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1.9k
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Comment: Comment: Mapping reads using kallisto - rna seq analysis
2.6 years ago by kalavattam ▴ 310
0
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0
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1.2k
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Comment: Comment: Reference Annotation GTF that includes piRNAs?
2.6 years ago by kalavattam ▴ 310
0
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1
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1.2k
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Comment: Comment: Reference Annotation GTF that includes piRNAs?
2.6 years ago by kalavattam ▴ 310
0
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1
reply
1.9k
views
Comment: Comment: Mapping reads using kallisto - rna seq analysis
2.6 years ago by kalavattam ▴ 310
0
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0
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1.7k
views
Comment: Comment: Quick way to get a field such as QNAME from the last read in a bam file?
18 months ago by kalavattam ▴ 310
0
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1
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1.7k
views
Comment: Comment: Quick way to get a field such as QNAME from the last read in a bam file?
2.6 years ago by kalavattam ▴ 310
0
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1
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1.7k
views
Comment: Comment: Quick way to get a field such as QNAME from the last read in a bam file?
2.7 years ago by kalavattam ▴ 310
2
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6
replies
1.7k
views
Quick way to get a field such as QNAME from the last read in a bam file?
bam samtools
18 months ago by kalavattam ▴ 310
2
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1
reply
1.2k
views
Fast way to use Samtools to sort a BAM file by queryname similar to `picard SortSam SORT_ORDER=queryname`?
samtools bam picard
3 months ago by kalavattam ▴ 310
0
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0
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11k
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Comment: Comment: How does salmon deal with decoy?
2.7 years ago by kalavattam ▴ 310
0
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0
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1.7k
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Comment: Comment: How to remove Mate mapped to a different chromosome
2.9 years ago by kalavattam ▴ 310
0
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0
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2.6k
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Comment: Comment: Duplicate reads remain in bam after picard MarkDuplicates --REMOVE_DUPLICATES tr
3.0 years ago by kalavattam ▴ 310
0
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1
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2.6k
views
Comment: Comment: Duplicate reads remain in bam after picard MarkDuplicates --REMOVE_DUPLICATES tr
3.0 years ago by kalavattam ▴ 310
1
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4
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2.6k
views
Duplicate reads remain in bam after picard MarkDuplicates --REMOVE_DUPLICATES true
deduplication qname fastq Picard bam
3.0 years ago by kalavattam ▴ 310
0
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0
replies
702
views
Align sample to two different assemblies, then classify pairs that differ significantly in alignment score
Bowtie2 classification mismatch alignment gaps
3.4 years ago by kalavattam ▴ 310
2
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1
reply
2.1k
views
Answer: Answer: How to study transposable elements expression relationship with its closest gene
3.4 years ago by kalavattam ▴ 310
1
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0
replies
2.3k
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Answer: Answer: How to analysis 4c seq 3c seq data
3.8 years ago by kalavattam ▴ 310
0
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0
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1.3k
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Answer: Answer: recent Hi-C databases
3.8 years ago by kalavattam ▴ 310
0
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0
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1.2k
views
Comment: Comment: Bioinformatics definition of TAD boundary
3.8 years ago by kalavattam ▴ 310
106 results • Page 2 of 3
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