User: HK

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HK20
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2 years, 1 month ago
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Posts by HK

<prev • 33 results • page 1 of 4 • next >
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NUmber of exons and their sequnece from given cordinates
... Hey All, I am using GRCh38.p7 reference genome using GENCODE realease 25 (ensemble 85 annotation(GTF)). I have a set of cordinates (transcripts) and i want to know how many and which exons lie in between the cordinates and then get the sequence (using the given annotation and assembly). Geting t ...
sequence exon written 13 days ago by HK20
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Comment: C: finding each pattern in a set of sequences
... Well i knw i have to use the loop on the localAlignment function, but as i an newbie i R so have some problems in using loop or any alterantive way. The logic in mind is using nested loops for(i in 1:length(pattern){ for(j in 1:length(subjects){ loaclAlignmentfunction }} # i. ...
written 9 weeks ago by HK20
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Comment: C: finding each pattern in a set of sequences
... @Bastien Herve Thanks for the reply, i have already used this function but as mentioned it actually matches p1 vs s1, p2 vs s2, p3 vs s3 nd p4 vs s4. whereas i need something different i.e (p1 vs s1,p1 vs s2, p1 vs s3, p1 vs s4), then take the 2nd pattern and match with all subjects (p2 vs s1, p2 v ...
written 9 weeks ago by HK20
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finding each pattern in a set of sequences
... Hey All, I am trying to find a pattern in a set of sequences. What i am trying to do is that first take the 1st sequence of the pattern and match it with all subjects one by one and give an output (p1 vs s1,p1 vs s2, p1 vs s3, p1 vs s4), then take the 2nd pattern and match with all subjects (p2 vs ...
R loop pattern subject programming written 9 weeks ago by HK20
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Comment: C: getting previous exon from gtf file
... @Kevin Blighe can you kindly check the corrected input and output, an help me with the solution ...
written 9 weeks ago by HK20
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Comment: C: getting previous exon from gtf file
... @Kevin Blighe i am corrected the input dataframes again, realized there was a mistake. I did made a unique eye i.e geneid_exon_num_start_end and then found the match between exon and gtf by using gft[which(gtf$geneid_exon_num_start_end %in% myexons$geneid_exon_num_start_end) Now when i have the ma ...
written 10 weeks ago by HK20
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Comment: C: getting previous exon from gtf file
... @cpad0112 i have corrected the input and output now. ...
written 10 weeks ago by HK20
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getting previous exon from gtf file
... Hey everyone, I have a dataframe with the my selected exon cordinates(dataframe=my exons) and a gtf dataframe (dataframe=gtf). I am trying to first find my exons from the gft and then once found trying to extract the previous exon from the gft as output. i have given an example below. #dataframe ...
gtf R exons written 10 weeks ago by HK20
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Intron cordinates requires for known exons
... Hey all, I am working on the genomics data and need some help with the cordinates of introns. I have a data frame of few exons(having start and end position) and i wanted to get the coordinates(start and end position) of the previous and next intron to the paticular exons. ![Exon intron cordinates ...
introns exons rna-seq written 12 weeks ago by HK20
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reverse complementary matches in two sequences.
... Hey All, I have a two DNA strings, and want to check if they reverse complementary to each other (or part of that). ![RCM is the reveser complimentary match][1]: https://ibb.co/e5pOKn As shown in this imagine, i have the sequence of the encircled part (grey) and want to find the highly reverse ...
alignment reverse complimentary sequence written 3 months ago by HK20 • updated 3 months ago by genomax51k

Latest awards to HK

Popular Question 13 days ago, created a question with more than 1,000 views. For small RNA seq annotation
Popular Question 9 months ago, created a question with more than 1,000 views. For small RNA seq annotation

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