User: Joel Wallenius

Reputation:
70
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Trusted
Location:
Sweden
Last seen:
1 month ago
Joined:
2 years, 5 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 2 of 7 • next >
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Comment: C: Is there a command line tool that can take an alignment fasta and input and outp
... You are so helpful! Thank you :)) My code has the same structure as yours, but I'm getting silly results where you get nice ones. My alignments are not centered, wrap to multiple lines, and the output page is not landscape oriented. Hmm... \documentclass[a4paper,oneside,12pt]{memoir} \usep ...
written 8 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
... Hey, ESpript was interactive in the CLI so I had to resort to texshade. It's... almost working well. Wasted a few hours on that it couldn't handle special characters in the sequence IDs, amongst other things. Anyway, now I only need to figure out how to properly center the image. Do you have any id ...
written 8 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 is quite beautiful! I shall keep this one... and if Espript proves troublesome I know what to do. Big thanks!! ...
written 8 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
... Yup... I guess I'm terrible at searching, but to be fair it's a bit of a stretch to have to navigate through "Online and web" to find what is offline and not web. -_- Big thanks though!!! ...
written 8 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
... Hey, I can't find a link to download Espript. It says in the FAQ that it's a web browser software? http://espript.ibcp.fr/ESPript/ESPript/esp_faq.php ...
written 8 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 am very OK with TeXing. Looking into Espript in the meantime. Thank you! ...
written 8 months ago by Joel Wallenius70
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Is there a command line tool that can take an alignment fasta and input and outputs an image?
... Hello! I've been trying to find a software that does what the post title describes, but without luck. I tried installing JalView but it won't install for some reason "Installer User Interface Mode Not Supported". I have hundreds of images to generate so going to a browser MSA viewer and manually s ...
fasta image alignment written 8 months ago by Joel Wallenius70 • updated 8 months ago by Joe16k
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AnnoVar with custom genomes?
... Hello! I am doing some variant calling on mice against mm10, but with some human genes added to the reference genome during mapping, because the mice are gene-edited. Obviously AnnoVar doesn't know what to do with these reads but I would still like to have somewhat informative output like syn or no ...
annovar written 8 months ago by Joel Wallenius70
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Comment: C: Where is the (hg19) reference data for transcript isoforms' relative abundances
... Sorry I forgot about this one. Thank you for spelling that out! It makes a lot of sense to me. I don't think I can make much use of it though since my PI is forcing me to use htseq, which doesn't count on the transcript level. Hmm... so the "TPM" I'm calculating (the lengths I use are just the sum ...
written 9 months ago by Joel Wallenius70
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Comment: C: Where is the (hg19) reference data for transcript isoforms' relative abundances
... But how exactly do they estimate the expression of each isoform? EM? Is it much more than a pure guess? Reads can't typically tell them apart... or are they looking at reads that overlap the exon boundaries as indicators maybe? TPM still uses the gene length in its calculation, no way around it. If ...
written 9 months ago by Joel Wallenius70

Latest awards to Joel Wallenius

Popular Question 8 months ago, created a question with more than 1,000 views. For The meaning of '0' allele frequency in vcftools output
Popular Question 22 months ago, created a question with more than 1,000 views. For The meaning of '0' allele frequency in vcftools output
Autobiographer 2.4 years ago, has more than 80 characters in the information field of the user's profile.

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