User: bernatgel

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bernatgel2.4k
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@bernatgel
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Posts by bernatgel

<prev • 139 results • page 1 of 14 • next >
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Answer: A: how i can make genetic marker frequency plot?
... Hi If you are trying to plot the frequencies (FRECUENCY_A and FRECUENCY_B) along the genome, take a look at [karyoploteR]( https://bioconductor.org/packages/karyoploteR/). With [kpPoints](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/Points/Points.html) you should be able to plot your ...
written 1 day ago by bernatgel2.4k
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Comment: C: Plotting Bedgraph with multiple chromosome
... Oh, I see the problem. bedGraph files are not supposed to have a header. If you delete the first line in your file it should work right away. Another option would be to use `toGRanges` from `regioneR`. data.bg <- toGRanges("34regions.bg") it should load the data without any problem, but wi ...
written 3 days ago by bernatgel2.4k
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Comment: C: Plotting Bedgraph with multiple chromosome
... You need to install and load rtracklayer BiocManager::install("rtracklayer") and library("rtracklayer") and then import should work. Also, it's "bedGraph" with a capital "G"!! ...
written 6 days ago by bernatgel2.4k
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Comment: C: Plotting Bedgraph with multiple chromosome
... Hi @jaqx008, When I said custom genome I was referring to your own genome. I've updated the response to include a bit more of information on how to do that. Hope this helps! Bernat ...
written 6 days ago by bernatgel2.4k
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Answer: A: Plotting Bedgraph with multiple chromosome
... Hi jaqx008 You should be able to plot it with [karyoploteR](https://bioconductor.org/packages/karyoploteR/), using a custom genome (with your 50 contig names) and probably [kpArea](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/Area/Area.html) to plot the data. You should first load th ...
written 7 days ago by bernatgel2.4k
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Answer: A: Create manhattan plot from .qassoc
... Hi @malteze, Seeing the error you post in the second image, the problem seems to be that you are not telling `read.table` to treat the first line as the column names. To do that, you should use `header=TRUE`. TEST <- read.table(file = "C:/Users/lenovo/Desktop/TEST.qassoc", quote = "\"", com ...
written 10 days ago by bernatgel2.4k
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Answer: A: Plotting CpG methylation
... Hi Chandan Kumar, To plot data like this you can use [karyoploteR](https://bioconductor.org/packages/karyoploteR/), an R/Bioconductor package to plot data over the genome. To plot on Arabidopsis thaliana you just need to install the [BSgenome package for TAIR9](https://bioconductor.org/packages/BS ...
written 6 weeks ago by bernatgel2.4k
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Answer: A: Question: How to calculate base count for each base in one spot in sam file
... If you have (or are willing to convert to) BAM files (I think it cannot work with SAM files) we usually use [bam-readcount](https://github.com/genome/bam-readcount) for this kind of data extraction. The output is a bit more complex (and informative) than what you are asking, but it's possible to par ...
written 9 weeks ago by bernatgel2.4k
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Comment: C: How to plot copy number variation profile in R?
... Ops! That was a bug in the package. It's been fixed and should be available in a couple of days via BiocManager. In the meantime, if you change your column name from "cell_0" to "lrr" it should work Sorry about that! :) ...
written 10 weeks ago by bernatgel2.4k
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Answer: A: Which softwares do you suggest to analysis CNV with Human660W-Quad_v1_H sap arra
... We have been using ASCAT with Illumina SNP-array data and we are quite happy with it, although in recent times we have been using also GAP. GAP is really painful to use (it's not a package per se but a series of scripts with quite a few hardcoded paths and filenames... but if you get to make it work ...
written 10 weeks ago by bernatgel2.4k

Latest awards to bernatgel

Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 4 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Great Question 4 months ago, created a question with more than 5,000 views. For karyoploteR: uncircle your genomes
Scholar 5 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 9 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Centurion 9 months ago, created 100 posts.
Good Answer 12 months ago, created an answer that was upvoted at least 5 times. For A: Viewing CNV read depth data along multiple chromosomes in a single plot via R
Scholar 12 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Scholar 12 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Appreciated 13 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 13 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Сalculating fold-enrichment of ChIP-seq peaks intersecting with promoters (vs. g
Appreciated 14 months ago, created a post with more than 5 votes. For A: Permutation test with gene size and GC contents
Scholar 14 months ago, created an answer that has been accepted. For A: Testing for over-representation of chip-peaks

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