User: rezaeir75

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rezaeir7510
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1 year, 6 months ago
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Posts by rezaeir75

<prev • 25 results • page 1 of 3 • next >
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Comment: C: BLAST configuration for siRNA off-target search
... I was hoping that someone gives me a benchmarking paper or a specific configuration for blasting siRNAs for off-target. If no one gives me that, I will go with trying different parameters to see what works better! ...
written 9 weeks ago by rezaeir7510
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Comment: C: BLAST configuration for siRNA off-target search
... the query length is 22bp. Just changing the overall settings to short sequence blast is enough? Should I change anything about mismatch tolerance? ...
written 9 weeks ago by rezaeir7510
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BLAST configuration for siRNA off-target search
... *I have several siRNA sequences that I need to find their off-targets.* - How can I efficiently use **NCBI BLAST** to find the off-targets? - Which **parameters** should I change from their default and change it to what value? - What genome or transcriptome human **database** I should use? ...
sequence blast written 9 weeks ago by rezaeir7510
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Comment: C: Extracting rows on basis of specific column values in R
... Because you are using a regular expression and filter doesn't understand regex directly. Wrap your regex in grepl and also give it the target column and wrap that in your filter function. ...
written 10 weeks ago by rezaeir7510
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... I'd like to add [this very nice post][1] myself. [1]: https://towardsdatascience.com/genome-assembly-the-holy-grail-of-genome-analysis-fae8fc9ef09c ...
written 10 weeks ago by rezaeir7510
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... Sorry. It is much harder to get an answer in bioinformatics sites compared to stackoverflow! I won't do it again ...
written 10 weeks ago by rezaeir7510
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... Thank you so much for introducing this tool. I also checked the BIRCH website and it seems very promising. I'll definitely try it but because I use WSL2 instead of a full linux, it may be harder to use a GUI software. ...
written 10 weeks ago by rezaeir7510
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... Thank you so much for the links. The first one is very interesting. I'll read their github repo, read their paper, and maybe even try it using some sample data. ...
written 10 weeks ago by rezaeir7510
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... This is very interesting. Is BIRCH both local and Open Source? If it is, I'll definitely learn how to use it. Also thanks for the tutorial link. ...
written 10 weeks ago by rezaeir7510
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Comment: C: Resources to learn genome assembly workflow for small genomes (like viruses)
... Thanks a lot for your answer. I'll check the coursera link but I've previously seen some of their bioinformatics content and it is very basic and I'd rather a combination of theory and hands-on practice. I'll definitely check the link to Bioinformatics DotCa channel. Regarding the Galaxy tutorial, I ...
written 10 weeks ago by rezaeir7510

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