User: fr

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fr100
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Posts by fr

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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 26 days ago by fr100
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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 27 days ago by fr100 • updated 27 days ago by bruss0
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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 6 weeks ago by fr100
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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 6 weeks ago by fr100
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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 6 weeks ago by fr100
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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 6 weeks ago by fr100 • updated 6 weeks ago by Prakash1.3k
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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 7 weeks ago by fr100
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Comment: C: Combine .bed files and keep columns / headers
... I really don't understand why, but now I can't even get the `NA`. I have used `\t` as delimiters in my input, and now I'm getting #cat output.txt chr1 1 2 1 1 1 chr1 2 5 1 0 0 chr1 10 11 1 1 0 chr1 50 51 1 1 1 chr10 2 3 0 0 1 ...
written 7 weeks ago by fr100
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Comment: C: Combine .bed files and keep columns / headers
... Thanks. I was able to get it working with dummy data above, but not with my own data. I hope to get there soon! Thanks a lot ...
written 7 weeks ago by fr100
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Comment: C: Combine .bed files and keep columns / headers
... Thanks so much @ATpoint, I'm almost there. However, I get only `1` and `NA` in `output.txt`, and don't know how to intersect it with the initial input files. Also, is the order of columns 4 and so on the same as that specified in `-i [file1.bed, file2.bed, file3.bed]`? It doesn't seem that the outpu ...
written 7 weeks ago by fr100

Latest awards to fr

Scholar 12 weeks ago, created an answer that has been accepted. For A: How to skip a genebank file that has no dna sequence?
Popular Question 3 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 3 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 5 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 7 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 7 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?
Voter 8 months ago, voted more than 100 times.
Popular Question 11 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 19 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: theory behind the differential expression
Popular Question 22 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 24 months ago, created a question with more than 1,000 views. For Any tools for predicting protein solvent exposure/accessibility?
Popular Question 2.4 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 2.4 years ago, created a question with more than 1,000 views. For BioPerl retrieves joined sequence incorrectly
Popular Question 2.8 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 4.0 years ago, created a question with more than 1,000 views. For How to retrieve gene sequences and their products from NCBI's FTP?
Scholar 4.5 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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