User: biostart

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biostart340
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Posts by biostart

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Comment: C: Correlation of two ChIP-seq signals?
... bin size 200 bp. I previously tried narrowing down to only gene bodies (see above), which did not help. I have now also tried to narrow down the analysis only to promoters, but the result is the same as before. ...
written 7 weeks ago by biostart340
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Comment: C: Correlation of two ChIP-seq signals?
... I was also thinking that this may be the case, so I narrowed down the correlation analysis only to gene bodies. As a result I get even stronger positive correlation genome-wide inside gene bodies, which still does not explain the negative correlation that I see by eye in the example genes. ...
written 7 weeks ago by biostart340
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Comment: C: Correlation of two ChIP-seq signals?
... The code is quite standard, e.g. I calculated correlations between BigWig files using deepTools (both bin-based and region-based), and I also calculated it using a custom code, with the same result (positive correlation). The by-eye analysis is definitely not representative, but it's kind of also im ...
written 7 weeks ago by biostart340
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Correlation of two ChIP-seq signals?
... Hi all, I am looking at two continuous ChIP-seq signals (think of histone modifications), and for several randomly selected example regions I see by eye that these signals are **anti-correlated** (peaks of one signal at locations of deeps of another signal). But when I calculate a proper correlatio ...
chip-seq written 7 weeks ago by biostart340 • updated 5 weeks ago by Prakash1.7k
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Comment: C: Problem mapping paired-end Illumina reads
... kmer content: ![k-mers][1] [1]: http://i65.tinypic.com/zlzzvq.png ...
written 12 months ago by biostart340
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Comment: C: Problem mapping paired-end Illumina reads
... ![GC content][1] [1]: http://i67.tinypic.com/105tb7k.png ...
written 12 months ago by biostart340
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Comment: C: Problem mapping paired-end Illumina reads
... ![per base sequence content][2] [2]: http://i66.tinypic.com/k35g1l.png ...
written 12 months ago by biostart340
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Comment: C: Problem mapping paired-end Illumina reads
... FastQC reports for both read 1 and 2 for the problematic samples look similarly problematic, I am posting the images below. Any idea how to correct this? ![FastQC quality score] [2] [2]: http://i67.tinypic.com/25k0itd.png ...
written 12 months ago by biostart340
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Comment: C: Problem mapping paired-end Illumina reads
... I can estimate the average DNA fragment length as ~150 based on the reads which successfully aligned ...
written 12 months ago by biostart340
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Comment: C: Problem mapping paired-end Illumina reads
... The numbers of reads is the same, but their quality seems to be different: I have mapped with Bowtie separately each of the two paired fastq files: for one file I've got 50% reads with at least one reported alignment, whereas for the second fastq file I've got 31% reads with at least one reported al ...
written 12 months ago by biostart340

Latest awards to biostart

Epic Question 12 months ago, created a question with more than 10,000 views. For GO analysis: DAVID vs GREAT vs GOrilla
Popular Question 12 months ago, created a question with more than 1,000 views. For Converting CpG methylation calls to average genome coverage
Popular Question 12 months ago, created a question with more than 1,000 views. For [solved] Bowtie mapping paired-end reads of different length
Popular Question 12 months ago, created a question with more than 1,000 views. For bedtools closest (output file format)
Popular Question 12 months ago, created a question with more than 1,000 views. For Gene Ontology without enrichment analysis
Popular Question 12 months ago, created a question with more than 1,000 views. For Problem mapping SOLiD reads with Bowtie1
Popular Question 14 months ago, created a question with more than 1,000 views. For [solved] Bowtie mapping paired-end reads of different length
Popular Question 17 months ago, created a question with more than 1,000 views. For [solved] Bowtie mapping paired-end reads of different length
Popular Question 17 months ago, created a question with more than 1,000 views. For bedtools closest (output file format)
Popular Question 17 months ago, created a question with more than 1,000 views. For Gene Ontology without enrichment analysis
Popular Question 17 months ago, created a question with more than 1,000 views. For BedTools can't find "hg19.genome"
Appreciated 2.7 years ago, created a post with more than 5 votes. For GO analysis: DAVID vs GREAT vs GOrilla
Great Question 2.7 years ago, created a question with more than 5,000 views. For GO analysis: DAVID vs GREAT vs GOrilla
Good Question 2.7 years ago, asked a question that was upvoted at least 5 times. For GO analysis: DAVID vs GREAT vs GOrilla
Popular Question 2.7 years ago, created a question with more than 1,000 views. For [solved] Bowtie mapping paired-end reads of different length
Popular Question 2.7 years ago, created a question with more than 1,000 views. For bedtools closest (output file format)
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Gene Ontology without enrichment analysis
Popular Question 2.7 years ago, created a question with more than 1,000 views. For BedTools can't find "hg19.genome"
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Merging many BAM files [solved]
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Splice site coordinates: where to get them?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For Is it typical to find a ~30 bp motif enriched in promoters of ~20 related genes?
Teacher 2.7 years ago, created an answer with at least 3 up-votes. For A: how to get TF binding affinity from ENCODE narrowPeak or broadPeak files?
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Merging many BAM files [solved]

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