User: Amirosein

gravatar for Amirosein
Amirosein70
Reputation:
70
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Trusted
Location:
UBC, Vancouver, CA.
Last seen:
1 year, 2 months ago
Joined:
3 years, 10 months ago
Email:
a***********@gmail.com

Posts by Amirosein

<prev • 40 results • page 2 of 4 • next >
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Comment: C: is there any fast and accurate read mapper which provides and easy-to-use API?
... What do you mean by taking a pipe as input? I want my program to include my own algorithm and a read aligner at the same time working together on every single read. ...
written 23 months ago by Amirosein70
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is there any fast and accurate read mapper which provides an easy-to-use API?
... Hello, I am wondering if the most famous read aligners provide easy-to-use APIs. More specifically, I am developing an algorithm for variant calling and I need to divide input reads and pass each read segment to the aligner and receive its location quickly. for example, instead of saving some read ...
read alignment written 23 months ago by Amirosein70
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Comment: C: how to write some sequences in a (.fq)-like file?
... yeah of course :) , because i want to use bowtie to find some fragments of a genome in another one, so for sending this fragments to bowtie i need to prepare them as a read ...
written 3.0 years ago by Amirosein70
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how to write some sequences in a (.fq)-like file?
... Hi I have a DNAStringset containing some sequences of length 25. i want to make an .fq file of it but first i need to add a "specific" header (which stored in a vector) for each read. the data is like this: A DNAStringSet instance of length 2 width seq name ...
write R writexstringset io read written 3.0 years ago by Amirosein70 • updated 3.0 years ago by mforde841.2k
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Comment: C: how to add lines to a plot gradually (ggplot2) ?
... sorry but Wrong! as you can see in my example, i want multiple distinct lines... i found my answer myself, i have to group lines and then use group parameter in geom_line() ...
written 3.0 years ago by Amirosein70
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how to add lines to a plot gradually (ggplot2) ?
... Hi I have and algorithm which found some new 2D lines in each iteration, i want to add this lines to ggplot frequently, i searched for it but i can't find a good example, i write it using normal plot and that's it: plot(c(0 , Len1), c(0, Len2), type= "n",xlim=c(0,Len1), ylim=c(0,Len2)) f ...
line R ggplot2 plot written 3.0 years ago by Amirosein70 • updated 3.0 years ago by Roman Luštrik80
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Comment: C: importing .SAM files into R (Rstudio)
... so why i should convert it ? if i can read it directly ? ...
written 3.1 years ago by Amirosein70
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importing .SAM files into R (Rstudio)
... Hi I have some .sam files as output of bowtie run. i want to read them into Rstudio. i searched for it but all i can find is about importing .bam files. some suggest converting .sam into .bam. is it the only way? and is this convertion lossless? thanks ...
R sam bowtie written 3.1 years ago by Amirosein70 • updated 3.1 years ago by geek_y10k
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VariantCalling with single sanger read
... Hi All I want to do VariantCalling but with a single sanger read in a single specific region (so i can't use routine VariantCalling pipelines). for example i have a sanger read from a region of a gene and i know that gene, now i want to tell Genomic Poisition of Homozygous and Heterozygous events. ...
indel snps variantcalling blast written 3.4 years ago by Amirosein70 • updated 11 months ago by trausch1.4k
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How to check new variants for functional effects?
... Hi all I'm writing a code in Rstudio/Bioconductor and i found some unreported variations from some patients, is there any easy way to predict functional effects of this changes? any package? specially i want to check them for pathogeneticity(?), like what SIFT and PolyPhen2 do, but inside Rstudio o ...
annovar snp variants written 3.4 years ago by Amirosein70 • updated 3.4 years ago by DG7.1k

Latest awards to Amirosein

Popular Question 14 months ago, created a question with more than 1,000 views. For detection of in/del in sanger sequencing
Popular Question 23 months ago, created a question with more than 1,000 views. For importing .SAM files into R (Rstudio)
Popular Question 23 months ago, created a question with more than 1,000 views. For how to add lines to a plot gradually (ggplot2) ?
Popular Question 23 months ago, created a question with more than 1,000 views. For Variant calling for sanger reads
Scholar 3.8 years ago, created an answer that has been accepted. For A: Retrieving overlaps inside a single dataset using foverlaps

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