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Comment: C: how to visualize rna-seq coverage track in igv?
4.8 years ago by Zee_S ▴ 60
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4.0k
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Comment: C: how to visualize rna-seq coverage track in igv?
5.1 years ago by Zee_S ▴ 60
2
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6
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4.0k
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how to visualize rna-seq coverage track in igv?
igv RNA-Seq coverage bam normalization
updated 5.1 years ago by ★ 18k • written 5.1 years ago by ▴ 60
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4.0k
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Comment: C: how to visualize rna-seq coverage track in igv?
5.1 years ago by Zee_S ▴ 60
1
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1
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1.2k
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STAR mapping statistics don't add up with samtools count
STAR read count samtools PE SE
updated 5.2 years ago by 15k • written 5.2 years ago by ▴ 60
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0
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918
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what does the alignment statistics of your RNA spike-in tell you about your sample of interest in two experimental conditions?
Spike-in RNA-seq STAR normalization
5.2 years ago by Zee_S ▴ 60
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Comment: C: Is there a way to get multiBigwigSummary with 1-based coordinates instead of 0-b
5.2 years ago by Zee_S ▴ 60
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1
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1.4k
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Comment: C: Is there a way to get multiBigwigSummary with 1-based coordinates instead of 0-b
5.2 years ago by Zee_S ▴ 60
2
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4
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1.4k
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Is there a way to get multiBigwigSummary with 1-based coordinates instead of 0-based?
Deeptools multiBigwigSummary
5.2 years ago by Zee_S ▴ 60
0
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0
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4.6k
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Comment: C: is 0-based start and 1-based end of bed format not compatible with htseq-count?
5.3 years ago by Zee_S ▴ 60
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1
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4.6k
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Comment: C: is 0-based start and 1-based end of bed format not compatible with htseq-count?
5.3 years ago by Zee_S ▴ 60
6
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11
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4.6k
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is 0-based start and 1-based end of bed format not compatible with htseq-count?
htseq-count index-error 0-based start bed to gtf
updated 5.3 years ago by ★ 3.9k • written 5.3 years ago by ▴ 60
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0
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4.6k
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Comment: C: is 0-based start and 1-based end of bed format not compatible with htseq-count?
5.3 years ago by Zee_S ▴ 60
0
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1
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4.6k
views
Comment: C: is 0-based start and 1-based end of bed format not compatible with htseq-count?
5.3 years ago by Zee_S ▴ 60
1
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1
reply
1.2k
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HT-seq-count default parameter to "score"secondary alignments contradicts its documentation that it ignores multi mappers by default. Not clear!
secondary alignment multimapping read HTSeq-count
5.3 years ago by Zee_S ▴ 60
0
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1
reply
1.8k
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How to divide a chromosome into arms and center?
chromsome arm center bed coordinates
6.1 years ago by Zee_S ▴ 60
0
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0
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2.6k
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Comment: C: How to add linear regression line and change the colors of my hexbin scatterplot
6.1 years ago by Zee_S ▴ 60
0
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4
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2.6k
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How to add linear regression line and change the colors of my hexbin scatterplot?
hexbin scatterplot linear regression R
updated 6.1 years ago by 12k • written 6.1 years ago by ▴ 60
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1
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2.6k
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Comment: C: How to add linear regression line and change the colors of my hexbin scatterplot
6.1 years ago by Zee_S ▴ 60
0
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1
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5.5k
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Comment: A: How to add a regression line and change colors in ggplot smoothscatter?
updated 6.2 years ago by 44k • written 6.2 years ago by ▴ 60
1
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6
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5.5k
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How to add a regression line and change colors in ggplot smoothscatter?
ggplot smoothscatter R
6.2 years ago by Zee_S ▴ 60
0
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1
reply
1.1k
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Deeptools plotCorrelation function bug?
deeptools plotCorrelation
6.2 years ago by Zee_S ▴ 60
2
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2
replies
3.0k
views
How to correlate chip seq peaks?
chip seq correlation pearson spearman peaks
updated 6.4 years ago by ★ 2.1k • written 6.5 years ago by ▴ 60
0
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0
replies
1.2k
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how to correlate RNAseq dataset to chipset dataset?
rnaseq chIPseq correlation
6.6 years ago by Zee_S ▴ 60
0
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0
replies
1.1k
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how to produce a cluster plot of rna-seq + chipseq data?
rnaseq chipseq correlation
6.7 years ago by Zee_S ▴ 60
0
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0
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2.7k
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Comment: C: How to do correlation analyses between RNAseq and ChIPseq library?
6.7 years ago by Zee_S ▴ 60
0
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0
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2.9k
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Comment: C: Pearson correlation between chIP-seq replicates is very poor- am I doing somethi
6.7 years ago by Zee_S ▴ 60
0
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0
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2.7k
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Comment: C: How to do correlation analyses between RNAseq and ChIPseq library?
6.7 years ago by Zee_S ▴ 60
3
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4
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2.7k
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How to do correlation analyses between RNAseq and ChIPseq library?
RNA-Seq ChIP-Seq correlation normalization
updated 6.7 years ago by ▴ 990 • written 6.7 years ago by ▴ 60
0
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0
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905
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Can one artificially increase read count per genomic bin for IP and Input libraries in order to prevent significant changes in log2ratio?
ChIP-Seq normalization
6.7 years ago by Zee_S ▴ 60
0
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1
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1.9k
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How to classify chIP-seq reads into gene bins?
RNA-Seq ChIP-Seq gene TPMScore normalization
updated 6.7 years ago by 105k • written 6.7 years ago by ▴ 60
2
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5
replies
2.9k
views
Pearson correlation between chIP-seq replicates is very poor- am I doing something wrong in the normalization?!
correlation ChIP-Seq pearson
updated 6.7 years ago by ▴ 730 • written 6.7 years ago by ▴ 60
0
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1
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2.9k
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Comment: C: Pearson correlation between chIP-seq replicates is very poor- am I doing somethi
6.7 years ago by Zee_S ▴ 60
0
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1
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1.3k
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Comment: C: is it necessary to normalize between a Paired-End and Single-End library?
6.7 years ago by Zee_S ▴ 60
1
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3
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1.3k
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is it necessary to normalize between a Paired-End and Single-End library?
RNA-Seq ChIP-Seq normalization
6.7 years ago by Zee_S ▴ 60
1
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1
reply
12k
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Comment: C: Chromosome Position From Ucsc Genome Browser
6.7 years ago by Zee_S ▴ 60
0
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1
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4.4k
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Comment: C: How to annotate repeats?
6.7 years ago by Zee_S ▴ 60
2
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12
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3.5k
views
6 follow
How to get the total genic and intergenic length of a chromosome?
genic intergenic length
updated 3.3 years ago by ▴ 40 • written 6.7 years ago by ▴ 60
0
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1
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3.5k
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Comment: C: How to get the total genic and intergenic length of a chromosome?
6.7 years ago by Zee_S ▴ 60
0
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1
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3.5k
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Comment: C: How to get the total genic and intergenic length of a chromosome?
6.7 years ago by Zee_S ▴ 60
0
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2
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3.5k
views
Comment: C: How to get the total genic and intergenic length of a chromosome?
updated 6.7 years ago by 148k • written 6.7 years ago by ▴ 60
0
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1
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3.5k
views
Comment: C: How to get the total genic and intergenic length of a chromosome?
6.7 years ago by Zee_S ▴ 60
0
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1
reply
1.2k
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how to get intergene coordinates for a single chromosome?
bedtools intersect intergene coordinates
6.7 years ago by Zee_S ▴ 60
8
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4
replies
4.4k
views
How to annotate repeats?
repeats annotation SINE LINE normalization
updated 6.7 years ago by ▴ 140 • written 6.7 years ago by ▴ 60
0
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1
reply
1.2k
views
Comment: C: Calculate the total genie length targeted in my chIP
6.7 years ago by Zee_S ▴ 60
0
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2
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1.8k
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How to compute log2ratio of IP/Input when Input has zero reads?
normalization log2ratio bedtools coveragebed Input
6.7 years ago by Zee_S ▴ 60
3
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5
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1.2k
views
Calculate the total genie length targeted in my chIP
ChIP-Seq Genic_length enrichment BEDtools
updated 6.7 years ago by 12k • written 6.7 years ago by ▴ 60
0
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1
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1.2k
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Comment: C: how to calculate the total genie length targeted in my chIP?
6.7 years ago by Zee_S ▴ 60
0
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0
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1.5k
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Where, When and How to use the "breadth of coverage" values reported per bin in BEDtools coverageBED?
bedtools bedtools_coverageBED bedtools_windowMaker
6.7 years ago by Zee_S ▴ 60
1
vote
1
reply
2.2k
views
How to calculate the correlation between two ChIP-seq INPUT datasets?
ChIP-Seq sequencing normalization correlation
6.7 years ago by Zee_S ▴ 60
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