User: johannes.ptok

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johannes.ptok100
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Posts by johannes.ptok

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Comment: C: Standard options for mapping with STAR in context of RNA-seq data analysis regar
... Would'nt the possibilty for wrong mapping be 3/4, when a read is mapped with just one nucleotide overlap? **EDIT:** Thanks for editing btw, this forum is great! :) ...
written 13 days ago by johannes.ptok100
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Comment: C: Standard options for mapping with STAR in context of RNA-seq data analysis regar
... Ok I will continue using the default settings than. However, I still can't wrap my head around why lowering the treshold for annotated junctions does not lead to missmapped reads at this position? How is this possible? Or does STAR prevent missmapping at positions of annotated junctions at another ...
written 13 days ago by johannes.ptok100
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Standard options for mapping with STAR in context of RNA-seq data analysis regarding splicing
... Hi, During my analysis of RNA-seq data regarding alternative splicing and splicing pattern, I came across some standard options of the STAR algorithm, which I could not quiet follow. --alignSJoverhangMin 8 (minimum overhang for unannotated junctions) --alignSJDBoverhangMin 1 (minim ...
splicing star options rna-seq written 13 days ago by johannes.ptok100 • updated 13 days ago by Devon Ryan76k
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Comment: C: Where can I download genomes of Retroviruses?
... No, but since the number of different retroviruses which affect humans is very low and my approach is very broad for now, I will just use HIV as a representative for retroviruses. Thanks :) ...
written 16 days ago by johannes.ptok100
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Comment: C: Where can I download genomes of Retroviruses?
... I will save the link you send, but right now I'm not interested in the reference sequence of for example HIV1 but in the sequnence of different subtypes of HIV1, like it is for other virus families in the database I mentioned. ...
written 16 days ago by johannes.ptok100
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Comment: C: Where can I download genomes of Retroviruses?
... I only found reference genomes, which had to be collected by copy and paste. For other viurs families, there are giant databases of viral genome subtypes, which can be downloaded, like here: https://www.viprbrc.org/brc/home.spg?decorator=vipr ...
written 16 days ago by johannes.ptok100
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Where can I download genomes of Retroviruses?
... Hi, for my comparison of viral genomes, I would like to download genomes of retroviruses, which infect humans. Unfortunatly, I do not find any genomes of retroviruses in any databases. I would be interested in the final viral DNA sequence after integration in the human genome. Until now, I only ...
genome database retrovirus written 16 days ago by johannes.ptok100 • updated 16 days ago by Jean-Karim Heriche14k
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Comment: C: Doing RNA folding online for 1200 nt long sequence
... Thanky you very much, I think my search missed the word "webserver". Could you maybe also recommend a programm/package, to do the calculation automatically in R? ...
written 9 weeks ago by johannes.ptok100
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Doing RNA folding online for 1200 nt long sequence
... Hi, I have a 1200 nt long RNA sequence and I would like to calculate the free energy for its structure, without downloading anything if possible. ...
rna rna-folding written 9 weeks ago by johannes.ptok100 • updated 9 weeks ago by Eric Lim390
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Comment: C: Download all intronless human genes.
... Hi, thank you for your fast reply! I just went to the Biomart website and downloaded all coding sequences, after adjusting the filter, that there should be only one transcript, and the transcript should be protein coding. So I think I now have what I wanted. However, I didn't quiet understand wha ...
written 9 weeks ago by johannes.ptok100

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