User: Bioinformatist Newbie

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Posts by Bioinformatist Newbie

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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hi, thank you for your prompt response. Please note that I have actually tried your given (also above-mentioned) example of custome geneset/pathway creation and finding its enrichment. And I am getting the warning message that I posted in my question, however, I think I should get a table of enrichm ...
written 4 months ago by Bioinformatist Newbie240
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Comment: C: Pathway Enrichment Analysis, Clustering and Scoring with pathfindR
... Hello @egeulgen Thank you for providing an interesting and easy-to-follow tutorial. I tried the given script for custom gene set analysis and I am getting the following error, could you please guide me if I am doing something wrong? I am copying-and-pasting the exact code that you shared: ## Te ...
written 4 months ago by Bioinformatist Newbie240
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Comment: C: how to compare two TF binding sites
... If you have peak files for respective TFs and conditions, you can use **Bedtools** [intersect][1] to get what you want. 1a: For overlap binding sites: `bedtools intersect -a TF1.peakFile -b TF2.peakFile > overlappingSites.bed` 1b: For individual binding sites: `bedtools intersect -a TF1.peakF ...
written 19 months ago by Bioinformatist Newbie240
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Comment: C: Peak calling with MACS for paired end DNase-seq data
... Thank you for replying. Can you please guide me towards any such reference of using unadjusted pvalue. From unadjusted p-value, do you mean something like `-p 0.5` or so. So that I get more peak but point in this case would be, are those peaks reliable enough? I have got this data from our collabora ...
written 20 months ago by Bioinformatist Newbie240
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Comment: C: Peak calling with MACS for paired end DNase-seq data
... Thank you for your suggestion. By trying this: `macs2 callpeak -t MUT1_sorted.bam -f BAMPE -g hs -n MUT1_WT1 -q 0.05 --nomodel --shift 27 --extsize 54` I get only 2574 peaks. I think this number is not reasonable. Let's say if I associate each peak to a gene, even then, only 2574 genes are accessibl ...
written 20 months ago by Bioinformatist Newbie240
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Comment: C: Peak calling with MACS for paired end DNase-seq data
... Thank you for replying. I think I am missing many peak regions even if I call peaks without using the control. Please see this [IGV Image][1]. As per my understanding, I should observe a peak for this region as many of the reads are mapping in this region but In actual I don't see a narrow peak for ...
written 20 months ago by Bioinformatist Newbie240
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Peak calling with MACS for paired end DNase-seq data
... I have a paired-end DNAseq data for wild-type and mutant conditions. I aligned the reads with GRCh38 genome by using BWA mem and wanted to call peaks from paired BAM file by using macs2 with `-f BAMPE`, but I am getting very few number of peaks (80 peaks with q-value 0.05) and I am unable to underst ...
macs2 paired-end dna-seq bwa written 21 months ago by Bioinformatist Newbie240 • updated 21 months ago by igor9.2k
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Comment: C: ChIP-Seq TSS Line Plot
... @Guangchuang Yu, can you please help me with this [question][1]? Thanks! [1]: https://www.biostars.org/p/307764/ ...
written 22 months ago by Bioinformatist Newbie240
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Comment: C: How to plot ChIP-seq Density vs Distance from TSS using Homer annoted files
... @Sinji Can you please help me with this [question][1]. Thanks [1]: https://www.biostars.org/p/307764/ ...
written 22 months ago by Bioinformatist Newbie240
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How to plot the TF binding occupancy around a specific regulatory region?
... I have an enhancer region of NANOG (chr12:6831533-6857455) and potential TF binding sites for some other TFs (SOX2, POU5F1, KLF4 and NANOG) in this enhancer region. I want to plot the location and distribution of peaks in this enhancer region, and [ChIPseeker][1] seems a reasonable option for me. Ho ...
chip-seq tf-binding plot written 22 months ago by Bioinformatist Newbie240

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Popular Question 15 months ago, created a question with more than 1,000 views. For How to find Minimum dominating set in a biological network
Popular Question 15 months ago, created a question with more than 1,000 views. For Chip-Seq (Transcription Factor) data resources
Popular Question 15 months ago, created a question with more than 1,000 views. For Identify target miRNA for a mRNA
Popular Question 15 months ago, created a question with more than 1,000 views. For Peak calling with MACS for DNase-seq data and Peak annotation by Homer
Popular Question 15 months ago, created a question with more than 1,000 views. For How to interpret a heatmap
Popular Question 15 months ago, created a question with more than 1,000 views. For R - Merge 2 network with different color nodes
Popular Question 15 months ago, created a question with more than 1,000 views. For Microarray analysis of CEL files with Log-transformation instead of GCRMA or RMA
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Popular Question 15 months ago, created a question with more than 1,000 views. For Microarray analyis of different platform (GPL96 vs. GPL3921)
Popular Question 15 months ago, created a question with more than 1,000 views. For Gene Expression Data of Disease vs. Control
Popular Question 18 months ago, created a question with more than 1,000 views. For How to find Minimum dominating set in a biological network
Popular Question 18 months ago, created a question with more than 1,000 views. For Chip-Seq (Transcription Factor) data resources
Popular Question 18 months ago, created a question with more than 1,000 views. For Peak calling with MACS for DNase-seq data and Peak annotation by Homer
Popular Question 18 months ago, created a question with more than 1,000 views. For How to interpret a heatmap
Popular Question 18 months ago, created a question with more than 1,000 views. For R - Merge 2 network with different color nodes
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Popular Question 21 months ago, created a question with more than 1,000 views. For Peak calling with MACS for DNase-seq data and Peak annotation by Homer
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Popular Question 23 months ago, created a question with more than 1,000 views. For Peak calling with MACS for DNase-seq data and Peak annotation by Homer
Popular Question 23 months ago, created a question with more than 1,000 views. For Peak calling with MACS for DNase-seq data and Peak annotation by Homer
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Popular Question 2.6 years ago, created a question with more than 1,000 views. For Peak calling with MACS for DNase-seq data and Peak annotation by Homer

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