User: elisheva

gravatar for elisheva
elisheva80
Reputation:
80
Status:
Trusted
Location:
Israel
Last seen:
1 month, 4 weeks ago
Joined:
3 years ago
Email:
e***********@gmail.com

undergraduate bioinformatics student

Posts by elisheva

<prev • 103 results • page 1 of 11 • next >
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Comment: C: Convert regex into DNAString object
... Because I use StringSet and I want the analysis to be as fast as possible. If I will convert any single interval into character, I guess it will be much slower. ...
written 4 months ago by elisheva80
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Convert regex into DNAString object
... Hi, I am trying to search for a pattern in a sequence in a way that a specific nucleotide won't be at the edges. For example, given the following sequence: x <- DNAString("TGCTTGCGCA") I want to extract all the occurrences of GC where there is no T before or after. ...
R bioconductor biostrings written 4 months ago by elisheva80
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Comment: C: Customising bedtools shuffle command
... Could you please upload some lines of your file? So it will be easier to understand what exactly do you want. ...
written 10 months ago by elisheva80
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Comment: C: Finding exons and introns sequences
... of course not. I am looking only on mammals. ...
written 13 months ago by elisheva80
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Comment: C: Finding exons and introns sequences
... Thank you for your response. But as I mentioned above, gff3 doesn't include introns coordinates for some reason. Therefore, I can't see how it will be helpfull. And one more thing, assuming I do have the coordinates and the complete genomes, I guess bedtools getfasta will more efficient for this cas ...
written 13 months ago by elisheva80
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Comment: C: finding exons and introns sequences
... I am working on 80 organisms from Ensembl db. So this is not practical to download their full genome. Besides, on their gff3/gtf files, there are no introns at all ): ...
written 13 months ago by elisheva80
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Comment: C: finding exons and introns sequences
... I tried it. But I have to say it's quite unclear for someone who is totally new to perl. Besides, I tried only to get transcript Ids of one chromosome and it takes about 3 minutes, so I guess for downloading full sequences it will take too much time. ...
written 13 months ago by elisheva80
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Finding exons and introns sequences
... Hello everybody!! I have to analyze exons' and intron's sequences of many organisms. My question is: what is the most efficient way to retrieve all those sequences in fasta format? Or in other words: which Database holds accessible information about e ...
genome ensembl sequence exon intron written 13 months ago by elisheva80 • updated 13 months ago by vkkodali1.5k
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Comment: C: bedtools intersect issue
... That's really weird, and yes, for the example I posted I get an output as I posted either. ...
written 15 months ago by elisheva80
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Comment: C: bedtools intersect issue
... I am using version: v2.26.0 ...
written 15 months ago by elisheva80

Latest awards to elisheva

Great Question 6 months ago, created a question with more than 5,000 views. For find ORF in sequence python
Popular Question 8 months ago, created a question with more than 1,000 views. For Best way to processing huge fasta files using python.
Epic Question 8 months ago, created a question with more than 10,000 views. For needleman-wunsch algorithm on python
Popular Question 10 months ago, created a question with more than 1,000 views. For Best way to processing huge fasta files using python.
Centurion 13 months ago, created 100 posts.
Popular Question 14 months ago, created a question with more than 1,000 views. For Best way to processing huge fasta files using python.
Popular Question 15 months ago, created a question with more than 1,000 views. For Best way to processing huge fasta files using python.
Popular Question 16 months ago, created a question with more than 1,000 views. For Best way to processing huge fasta files using python.
Great Question 18 months ago, created a question with more than 5,000 views. For needleman-wunsch algorithm on python
Popular Question 18 months ago, created a question with more than 1,000 views. For Writing a csv file python
Supporter 20 months ago, voted at least 25 times.
Popular Question 24 months ago, created a question with more than 1,000 views. For find ORF in sequence python
Popular Question 2.6 years ago, created a question with more than 1,000 views. For needleman-wunsch algorithm on python

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