User: Joel Wallenius

Reputation:
10
Status:
New User
Location:
Sweden
Last seen:
an hour ago
Joined:
1 year, 6 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 • 39 results • page 2 of 4 • next >
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... The super computer I'm working with does not support the latest GATK so I have to use 3.6. The best practices guide includes the indel realignment and base recalibrations as far as I can see on their web page. Unless SAMtools mpileup performs the recalibration automatically without being asked to, I ...
written 29 days ago by Joel Wallenius10
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... The commands for VarScan do not matter as it's a later step. I will paste the commands tomorrow when I'm at work again! ...
written 29 days ago by Joel Wallenius10
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... Changed the title and added command! ...
written 29 days ago by Joel Wallenius10
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Comment: C: Approximately following the GATK recommended workflow for DNA sequence data, my
... Changed the title and added command! ...
written 29 days ago by Joel Wallenius10
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Approximately following the GATK recommended workflow for DNA sequence data, my mpileup output files are empty
... Hello! I've googled for hours but haven't found a solution that worked for me. I have some raw human DNA paired-end data in fastq format, then I use these programs in this order: Trimmomatic (trim the reads) BWA (map the reads to hg19) SAMtools (sorting and indexing) Picard (duplicate marking) GAT ...
genome next-gen snp sequencing written 29 days ago by Joel Wallenius10
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Comment: C: Given a list of RefSeq homo sapiens mRNA transcripts, what is the simplest way t
... Sadly I can't rely on the protein alignments though I know they are better suited for homology in most cases. I must go by the transcripts since what I'm interested in is the exact conservation of a base-pair sequence motif. I'm starting to suspect that I shouldn't worry too much about finding the ...
written 12 months ago by Joel Wallenius10
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Comment: C: Given a list of RefSeq homo sapiens mRNA transcripts, what is the simplest way t
... I am completely unfamiliar with these programs. Like you say it seems very complicated. I was thinking that a question such as mine would have been asked many times before. Why would the answer be so complex, then? :/ ...
written 12 months ago by Joel Wallenius10
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Given a list of RefSeq homo sapiens mRNA transcripts, what is the simplest way to get the corresponding sequences from some other related species?
... Hello! I have a list of RefSeq accession numbers of mRNA transcripts, all from homo sapiens, and would like to, for each transcript, get the corresponding transcript (and its sequence) from a number of related species like mouse rat cow monkey etc. I can't imagine that there isn't already a databa ...
alignment orthology transcriptome written 12 months ago by Joel Wallenius10
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Interpreting the output of an mRNA structural motif search algorithm
... Hello! I am searching for motifs in some hundreds of mRNA sequences. I couldn't find any, so now I'm searching for structural motifs instead. I am not familiar with any such software so I just used the first one that worked without hassle - 'RNAProfile'. Its output includes some patterns like (((. ...
mrna motif structure written 14 months ago by Joel Wallenius10 • updated 14 months ago by Martombo2.4k
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Comment: C: Given a protein domain, like a TPR or zinc finger or some other one, can you pre
... That is remarkably close though. I tested it, it couldn't find any significant matches. Perhaps TPR regions are way too diverse for such a tool... ...
written 15 months ago by Joel Wallenius10

Latest awards to Joel Wallenius

Popular Question 11 months ago, created a question with more than 1,000 views. For The meaning of '0' allele frequency in vcftools output
Autobiographer 19 months ago, has more than 80 characters in the information field of the user's profile.

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