User: fr

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fr110
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Posts by fr

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How to export more than 1000 entries in IPA
... I have performed a miRNA targetscan, but every time I try to export the results I can only export 1000 (out of the 65 thousand rows). How do you export more than 1000 entries? ...
ingenuity pathway analysis ipa written 4 days ago by fr110
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Visualizing bigwig tracks
... I want to see how bigwig tracks look, but I'm not sure I'm doing things properly. When I look at them in WashU with default properties I see the following: This shows the reads per region. The maximum of 1 in the YY axis is given because it is showing the mean of all the reads (I assume), and no sm ...
chip-seq rna-seq written 19 days ago by fr110 • updated 18 days ago by colin.kern650
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Comment: C: EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and lab
... Is there any chance to change tick intervals for both horizontal and vertical axes? And thanks a lot this is awsome! ...
written 3 months ago by fr110
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Comment: C: Homer annotatePeaks on genomic regions
... This is not my case, my chromosomes are written as `chr1` too. I really don't understand what's wrong here ...
written 4 months ago by fr110
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Homer annotatePeaks on genomic regions
... I'm trying to annotate whole genomic regions, whose coverage I have computed before, from `.bed` files. To do so I'm using annotatePeaks.pl myfile.bed mm10 -noadj -fragLength 130 -annStats my_stats.txt > output.txt Where my `.bed` file has the correct format: BED files should have at ...
homer annotatepeaks chip-seq written 4 months ago by fr110 • updated 4 months ago by bruss20
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Comment: C: How to bin my count data for the entire genome?
... @Prakash, thanks a lot for your suggestion. Just to make sure, you mean something like this: bedtools makewindows -g mm10.txt -w 50000 > binned_genome.bed bedtools coverage -a binned_genome.bed -b myfile.bed -sorted -g mm10.txt My question is then: how are the summaries done? For inst ...
written 5 months ago by fr110
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Comment: C: RNAseq: Fisher-exact test with Benjamini-Hochberg multiple-testing correction us
... I understand. However, DESeq, edgeR, or limma should give you more robust results than Fisher's exact test from my understanding. My suggestion is: Perform the Fisher's exact test > correct its p values as @Jean-Karim said below; Compare your significant (FDR < 0.05?) genes with those that com ...
written 5 months ago by fr110
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Comment: C: RNAseq: Fisher-exact test with Benjamini-Hochberg multiple-testing correction us
... Ankit, may I ask why do you want to use Fisher's instead of those tools? ...
written 5 months ago by fr110
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How to bin my count data for the entire genome?
... I'm trying to represent my ChIP-Seq counts, normalized or not, in specific genomic bins but don't know how to do so. I have already processed my data, and have used `findPeaks` followed by `pos2bed.pl` to produce `.bedGraph` files that contain this info. However, I'd like to have counts summarized ...
genome homer next-gen chip-seq sequencing written 5 months ago by fr110 • updated 5 months ago by Prakash1.7k
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Comment: C: Combine .bed files and keep columns / headers
... Indeed. Thanks a lot, both your post and @ATpoint's below were quite useful. I got it working but for my purposes I think `--partition` was better than `merge` ...
written 5 months ago by fr110

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Popular Question 19 days ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Scholar 6 months ago, created an answer that has been accepted. For A: How to skip a genebank file that has no dna sequence?
Popular Question 6 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
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Popular Question 10 months ago, created a question with more than 1,000 views. For How to debug (and solve) Bioperl problems when a gbk file doesn't have the genome?
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Popular Question 14 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
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Commentator 2.0 years ago, created a comment with at least 3 up-votes. For C: theory behind the differential expression
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
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Popular Question 2.7 years ago, created a question with more than 1,000 views. For How to debug (and solve) Bioperl problems when a gbk file doesn't have the genome?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For BioPerl retrieves joined sequence incorrectly
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Scholar 4.8 years ago, created an answer that has been accepted. For A: How to skip a genebank file that has no dna sequence?
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