User: konkelzach

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konkelzach10
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Twitter:
mycodelic
Last seen:
5 months, 3 weeks ago
Joined:
10 months, 1 week ago
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k*********@protonmail.com

Posts by konkelzach

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Orthofiller failing `Error: hmmerfm is not a recognized sequence database file f
... I tried two different installations of hmmer 3.2.1 ...
written 7 months ago by konkelzach10
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Comment: C: Orthofiller failing `Error: hmmerfm is not a recognized sequence database file f
... It doesn't work for some of the `gff`s I'm working with, so for uniformity I wrote one that does. This had to be done for a previous analysis as well and it worked, however, the sources of some of the `gff`s in that analysis are different than this one. ...
written 7 months ago by konkelzach10
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Orthofiller failing `Error: hmmerfm is not a recognized sequence database file format`
... I have tried different `hmmer` binaries, but `orthofiller` keeps failing with: `Error: hmmerfm is not a recognized sequence database file format` I suspect there is some sort of integration problem with `nhmmer` and `orthofiller`, but I'm curious if anyone has run into this problem using `orthofil ...
nhmmer orthofiller hmmerfm error hmmer written 7 months ago by konkelzach10
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Answer: A: Choosing a de novo assembly for DGE analysis
... Out of these two, I would definitely choose K-mer 31. I think the decrease you're seeing in complete and single-copy BUSCOs is because more fragmented BUSCOs have been assembled into duplicate BUSCOs. ...
written 8 months ago by konkelzach10
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Answer: A: HMMER installed with conda: no tutorial folder
... Conda doesn't package code the same way the creator makes it. It basically creates the necessary binaries and preserves their dependencies in its own directory structure. You will have to go into the conda directory `$CONDADIR/env/hmmer` and search each sub directory for the tutorials folder. There ...
written 10 months ago by konkelzach10
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Comment: C: HMMER installed with conda: no tutorial folder
... conda is a python environment manager and its repository (channel) bioconda hosts premade environments of bioinformatic software. ...
written 10 months ago by konkelzach10
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Comment: C: Failure of MinKNOW installation on Ubuntu 18.04
... you could try `apt-get update -o Acquire::https::mirror.oxfordnanoportal.com/apt::Verify-Peer=false` or `apt-get update -o Acquire::https//mirror.oxfordnanoportal.com/apt::Verify-Peer=false` otherwise run a websearch for `Certificate verification failed: The certificate is NOT trusted. The certific ...
written 10 months ago by konkelzach10
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Comment: C: cannot make BLAST database using makeblastdb command line tool
... if this is one chromosome, you should only have one sequence in the fasta. you can count the number of sequences in your fasta via `grep '>' custom_hg19.fa | wc -l` ...
written 10 months ago by konkelzach10
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Answer: A: Failure of MinKNOW installation on Ubuntu 18.04
... See [this][1] stackexchange answer. A workaround is to run `apt-get update -o Acquire::https::mirror.oxfordnanoportal.com:apt::Verify-Peer=false` I'm not using Debian so I can't verify my format of `https://mirror.oxfordnanoportal.com/apt` in the above command is correct. Someone else care to chi ...
written 10 months ago by konkelzach10
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Answer: A: Learn python programming
... I learned from the MIT OpenCourseWare course on python on youtube. They have links to homework and it's completely free. Ultimately, it comes down to taking what you learn and applying it to a problem you're interested in. You really only need to learn data types, data structures, `if` commands, an ...
written 10 months ago by konkelzach10

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