User: Joel Wallenius

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Location:
Sweden
Last seen:
2 days, 10 hours ago
Joined:
2 years, 4 months ago
Email:
j************@gmail.com

MSc in Bioinformatics at Lund University.

Primarily interested in solving the aging problem. Eternal youth for everybody woop woop!

Background in astrophysics. I would rather program than think about study designs.

Posts by Joel Wallenius

<prev • 61 results • page 1 of 7 • next >
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Comment: C: Best alignment software for mapping short DNA reads to transcriptome?
... I'll do that, then. Thanks :-] ...
written 2 days ago by Joel Wallenius70
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Comment: C: Best alignment software for mapping short DNA reads to transcriptome?
... I joined this project late so I can't motivate the reasons why we have the data we have. We have RADseq DNA reads from all over the genome, and now we want to know approximately what percentage of those reads are within coding DNA. I can't think of a better analysis than mapping to CDS or ESTs, desp ...
written 4 days ago by Joel Wallenius70
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Comment: C: Best alignment software for mapping short DNA reads to transcriptome?
... How would that help? I'm unfamiliar with ESTs but based on what Wikipedia says they're just fragments of cDNA, i.e. they map to transcripts, so they're having the same problem my cDNA sequences in my transcriptome do. :( Am I missing something? ...
written 4 days ago by Joel Wallenius70
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Comment: C: Best alignment software for mapping short DNA reads to transcriptome?
... There is no reference genome I'm afraid... the dinoflagellate genome is enormous, I find only bits and pieces of it at NCBI. I have the transcriptome only The transcriptome is CDS, sadly. I suppose this introduces a risk of false positives as the organism is a eukaryote, with exons all over the pla ...
written 5 days ago by Joel Wallenius70
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Best alignment software for mapping short DNA reads to transcriptome?
... Hello! I googled but found only issues of RNA read quantification, which is fair enough but not the help I would like. I'm just curious what percentage of my DNA reads are within my organism's transcriptome. I was going to do it with BWA but then I read that BWA is for short reads vs a large genom ...
transcriptome alignment dna written 5 days ago by Joel Wallenius70
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Comment: C: Is there a command line tool that can take an alignment fasta and input and outp
... Heyo, I got in touch with him. Turns out if you put e.g. \usepackage{tglpagella} in the header, that becomes the 'default' font for the TexShade env, and the default font is called with 'rm', apparently (I thought 'rm' was for roman or something): \setfont{names}{**rm**}{md}{up}{tiny} And now it w ...
written 7 months ago by Joel Wallenius70
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Comment: C: Is there a command line tool that can take an alignment fasta and input and outp
... That email worked! Thank you and I will let you know what he says about this :-] ...
written 7 months ago by Joel Wallenius70
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Comment: C: Is there a command line tool that can take an alignment fasta and input and outp
... Yeah I have successfully used fontspec and eg tglpagella in a minimal Latex script, but when I use it inside the texshade environment everything goes bonkers. Do you have a fresh e-mail address to the writer of texshade? I only find old ones that cause a bounce... ...
written 7 months ago by Joel Wallenius70
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Comment: C: Is there a command line tool that can take an alignment fasta and input and outp
... I'll see if I can get in touch with him then! If I change back to LaTeX I can get it working OK, actually. Too bad... I thought XeTeX and LuaTeX were supposed to build on LaTeX, not diverge from it!? :( I tried the solution by Carlisle but get this error regardless of whether I use LaTeX or XeLaTe ...
written 7 months ago by Joel Wallenius70
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Comment: C: Is there a command line tool that can take an alignment fasta and input and outp
... I'm creating a pdf with xelatex through latexmk because I need to use special fonts that weren't available in pdflatex. Pastebin fasta: https://pastebin.com/xgNxMMRv I then convert the pdf to jpg but that's unimportant since the pdf is unsatisfactory: https://ibb.co/LNGHG7Y I have to leave work no ...
written 7 months ago by Joel Wallenius70

Latest awards to Joel Wallenius

Popular Question 7 months ago, created a question with more than 1,000 views. For The meaning of '0' allele frequency in vcftools output
Popular Question 21 months ago, created a question with more than 1,000 views. For The meaning of '0' allele frequency in vcftools output
Autobiographer 2.3 years ago, has more than 80 characters in the information field of the user's profile.

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