User: davide.chiarugi

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Posts by davide.chiarugi

<prev • 24 results • page 1 of 3 • next >
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Comment: A: STAR quantMode geneCounts: weird outcomes
... This would explain the cases in which you map on meta features and/or you have reads coming from both the sense and antisense RNA overlapping each other. The GFF is unlikely to have overlapping features because it is associated to the Human genome. Moreover I am mapping on features instead of meta f ...
written 6 weeks ago by davide.chiarugi20
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Comment: C: STAR quantMode geneCounts: weird outcomes
... I have just completed the post: it was submitted incomplete by accident ...
written 6 weeks ago by davide.chiarugi20
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STAR quantMode geneCounts: weird outcomes
... I have ran STAR 2.5.0a on my bulk RNA-seq data, obtained using a single-end stranded library preparation strategy. I have set --quantMode GeneCounts, to obtain the counts from the ''embedded'' htseq-count. I have obtained results like the following: ---------- N_unmapped 146273 ...
htseq-count star rna-seq written 6 weeks ago by davide.chiarugi20
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Comment: C: Colouring a string
... I apologise again for the bad formulation of my question. Initially, I thought that the main problem was to generate the string and not to save the output and, thus, I preferred not to bother people about the second issue. My bad. ...
written 8 weeks ago by davide.chiarugi20
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Comment: C: Colouring a string
... Tank you to everyone for your help: at the end, I thik I'll opt out for the screenshot solution. I'll try also RamRS suggestion about textGrob and, if I'll obtain some interesting results, I'll let you know. Again, thank you !!! ...
written 8 weeks ago by davide.chiarugi20
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Comment: C: Colouring a string
... Yes, at the end I would like to obtain a figure to put in a paper/presentation. ...
written 9 weeks ago by davide.chiarugi20
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Comment: C: Colouring a string
... Apologies for the bad formulation. I asked for colours in general and different solutions have been proposed. Among these, I have followed what looked the most suitable for me. What I am aiming to do is: 1. create the coloured string, as reported in the original question 2. save the string in a fil ...
written 9 weeks ago by davide.chiarugi20 • updated 9 weeks ago by RamRS19k
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Comment: C: Colouring a string
... And now, the further step: how would you save the output in a (image) file ? With the options I have tried I can export only a black string and not the coloured one .... ...
written 9 weeks ago by davide.chiarugi20
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Comment: C: Colouring a string
... Thank you so much: I am actually making the rest of the analysis in R and this turns out to be the best solution for me ! ...
written 9 weeks ago by davide.chiarugi20
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Colouring a string
... Imagine I have a DNA sequence (e.g., dummy and short, ATTATGCGGGGAATTT ) and I would like to colour the different nucleotides with different coluours, given that I have a vector indicating the position of the nucleotides to be coloured: (1,3,6,7,8,10) <- to be coloured in red (2,4,5,12) <- t ...
genome sequence written 9 weeks ago by davide.chiarugi20 • updated 9 weeks ago by jrj.healey9.1k

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