User: davide.chiarugi

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3 years, 2 months ago
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Posts by davide.chiarugi

<prev • 25 results • page 1 of 3 • next >
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Job: Computational Biologist at the Institute of Metabolic Science, University of Cambridge (UK)
... We are seeking a Computational Biologist to join the Metabolic Research Laboratories (MRL) Bioinformatics and Biostatistics (Bio2) Core Facility, a scientifically complex facility pursuing data driven scientific research projects, (also in collaboration with Astra Zeneca and other research partners ...
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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 8 months 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 8 months 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 8 months 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 months 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 months 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 8 months 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 8 months ago by davide.chiarugi20 • updated 8 months ago by RamRS22k
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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 8 months 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 8 months ago by davide.chiarugi20

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Popular Question 7 weeks ago, created a question with more than 1,000 views. For SAM file: same reads ID, slightly different sequence

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