User: jon.brate

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jon.brate250
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Posts by jon.brate

<prev • 83 results • page 1 of 9 • next >
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Comment: C: About calculating the GC content in a sliding window
... Thanks, I'll check it out. > GC content would be an average across the window size you are > choosing. I assume the -s option is step-size for bedtools makewindow. > If you were selecting a 100 bp window then you get the GC% across > initial 100 bp window. You then slide the window ove ...
written 9 weeks ago by jon.brate250
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Comment: C: About calculating the GC content in a sliding window
... Is there an alternative to a sliding window? I need to use some kind of a collection of nucleotides to calculate frequencies? If you know of any better methods to calculate GC content for every base I would be very happy. ...
written 9 weeks ago by jon.brate250
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About calculating the GC content in a sliding window
... I want to plot the GC content along a genome contig. And since it's not possible to estimate percentage or fractions of a single position I need to use some sort of window along the contig to estimate. I found [this page](https://wiki.bits.vib.be/index.php/Create_a_GC_content_track) which uses `bedt ...
bedtools gccontent written 9 weeks ago by jon.brate250
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Comment: C: How to create alignment of UTR's for use in TargetScan?
... Hey, No, haven't done any more on this yet. But I guess what I will do is to run OrthoFinder or some other tool to identify orthologues. And then simply align the UTR's of each ortholog using MAFFT or something. But the exact procedure I haven't figured out yet. Let me know if you will do something ...
written 16 months ago by jon.brate250
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How to create alignment of UTR's for use in TargetScan?
... Hi, I want to run TargetScan on a non-model species. I have transcriptomes of several closely related species and can extract the UTRs. But I am not sure what's the best way to create the necessary alignment? I guess I have to first identify the correct homologous UTRs and give them the same name a ...
targetscan mirna written 19 months ago by jon.brate250
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Comment: C: Trying to get access to the Trinity R commands...
... Thanks, I began installing a local copy of Trinity (on my Macbook), but I had problems compiling it so I stopped. Any experience installing Trinity locally? ...
written 21 months ago by jon.brate250
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Comment: C: Trying to get access to the Trinity R commands...
... Thanks, I found those, but I was actually looking for the R commands which are generated with the different perl scripts under the Differential Genexpression (I think a file called RScript is generated after running the perl script). These are no magic commands, but I am just interested in learning ...
written 21 months ago by jon.brate250
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Trying to get access to the Trinity R commands...
... On the server I use it is not so easy to install the necessary R packages when using `R --vanilla`, so I can't run the Trinity perl scripts which uses R for differential gene expression and visualizations (basically everything described [here](https://github.com/trinityrnaseq/trinityrnaseq/wiki/Trin ...
trinity rna-seq R written 21 months ago by jon.brate250
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Comment: C: Error Runnin miRDeep2
... Sorry for the late answer, I am not sure I understand your problem. My error was about the reference genome, not the miRNAs. And I am not sure which 'b' character you refer to, the one in the miRNA name? ...
written 21 months ago by jon.brate250
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Comment: C: What is Trimmomatic -validatePairs, and how to use it?
... Ok, I'll check it out. Thanks for the advice :) ...
written 2.4 years ago by jon.brate250

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Epic Question 16 months ago, created a question with more than 10,000 views. For Is the Picard SortSam queryname or coordinate equivalent to samtools sort -n?
Student 16 months ago, asked a question with at least 3 up-votes. For Is the Picard SortSam queryname or coordinate equivalent to samtools sort -n?
Epic Question 19 months ago, created a question with more than 10,000 views. For Extract gene sequences from gff3 file and reference fasta
Great Question 20 months ago, created a question with more than 5,000 views. For Is the Picard SortSam queryname or coordinate equivalent to samtools sort -n?
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Great Question 2.3 years ago, created a question with more than 5,000 views. For How to extract the longest isoform from multi fasta file
Student 2.3 years ago, asked a question with at least 3 up-votes. For Plot statistics from gtf/gff file
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Popular Question 3.0 years ago, created a question with more than 1,000 views. For How to get different colors on coverage tracks in IGV
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Great Question 3.7 years ago, created a question with more than 5,000 views. For Extract gene sequences from gff3 file and reference fasta
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