## User: Konstantinos Yeles

Reputation:
20
Status:
New User
Location:
University of Salerno, Salerno, Italy
Scholar ID:
Last seen:
17 hours ago
Joined:
3 years, 4 months ago
Email:
y*****************@gmail.com

PhD student

#### Posts by Konstantinos Yeles

<prev • 64 results • page 1 of 7 • next >
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Comment: C: Ranges from a fasta file
... Thank you for the time you spent. Well, I try to make an object from 3 different files (the fasta with the sequences, the gr_obj with coordinates in the genome and another table with read sequences from smallRNAseq) in order to plot something like coverage but for each different sequence of ind ...
written 6 days ago by Konstantinos Yeles20
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Comment: C: Ranges from a fasta file
... So names in the "fasta" file should have chr names and not something like smallRNA IDs e.g.: >piR-hsa-1 AGAAGACATTCGTGGAGGCGTC >piR-hsa-2 ACGCCTCCACGTAGTGTCTT >piR-hsa-3 ACGCCTCCACGAGTGTCTT ...
written 6 days ago by Konstantinos Yeles20
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Comment: C: Ranges from a fasta file
... Thank you! Probably naive problem but I get : BSgenome::getSeq(fasta,gr_obj) Error: subscript contains invalid names table(names(gr_obj)%in%names(fasta)) TRUE 53 sum(names(fasta)%in%names(gr_obj)) [1] 29 any suggestions on where to identify the proble ...
written 6 days ago by Konstantinos Yeles20
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Comment: C: Ranges from a fasta file
... rtracklayer::getSeq(fasta,gr_obj) Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'getSeq' for signature'DNAStringSet' > Biostrings::getSeq(fasta,gr_obj) Error in (function (classes, fdef, mtable) : unable to find an inh ...
written 6 days ago by Konstantinos Yeles20
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... I imported a fasta file using readDNAStringSet : fasta <- readDNAStringSet("~/piRbase.fa") fasta@ranges group start end width names 1 1 28720989 28721013 25 piR-hsa-1000547 2 1 42817439 42817467 29 piR-hsa-1483697 3 1 432 ...
written 6 days ago by Konstantinos Yeles20 • updated 6 days ago by Martin Morgan ♦♦ 22k
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... Maybe, you find useful these two packages: 1. https://github.com/sa-lee/plyranges 2. https://github.com/const-ae/tidygenomics ...
written 22 days ago by Konstantinos Yeles20
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... Dear Aaron, thank you for your answer!! Unfortunately, I just discussed with the experimentalist; the spike-ins haven't been added to each sample proportional to the number of cells. At least now I could suggest that for future experiments. But with this data, is it correct to proceed with the work ...
written 9 weeks ago by Konstantinos Yeles20
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Comment: C: Data import with read.delim
... Dear Justin, If you still need to read several txt files at once, I recommend you to read this or this. Furthermore, if you are new to this please  consider reading at least one workflow on how to  perform downstream analysis. RNA-seq workflow: gene-level exploratory analysis and differential expre ...
written 9 weeks ago by Konstantinos Yeles20
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... design component1.tre component1.unt component2.tre component2.unt total.tre total.unt sample1 1 0 0 0 0 0 sample2 0 1 0 0 0 0 sample3 1 ...
written 9 weeks ago by Konstantinos Yeles20
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