User: skymningen

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skymningen330
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Germany
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5 years, 2 months ago
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7 years, 8 months ago
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passionate professional bioinformatician and hobby molecular biologist

Posts by skymningen

<prev • 44 results • page 2 of 5 • next >
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Comment: C: Bcftools Back And Forth Conversion Error
... Ah, it is basically the same as for samtools. I could have thought of that. Edit: I just checked my Galaxy wrapper and realised that I already used -Sb there, and it still didn't work. Unfortunately I cannot test it right now on command line, due to some server problems. ...
written 7.2 years ago by skymningen330
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Bcftools Back And Forth Conversion Error
... I have been trying to convert bcf and vcf files back and forth with bcftools for testing purposes. So, first I ran a basic samtools mpileup on Galaxy, resulting in "test.bcf". After converting this file back to vcf in Galaxy, reconverting it to bcf did not work, so I downloaded the file and tried it ...
bcftools written 7.2 years ago by skymningen330 • updated 7.2 years ago by John Marshall2.1k
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Comment: C: Problem Adding Qualifiers To A Genbank File With Python
... I think it will be fine for "many" as in 5 to 10, but if it's more around 200 you might have to get back to another solution. ...
written 7.2 years ago by skymningen330
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Comment: C: Problem Adding Qualifiers To A Genbank File With Python
... I remember that using Artemis ( http://www.sanger.ac.uk/resources/software/artemis/) you can load your Genbank file and add qualifiers (such as locus_tag) to all or specifically filtered features (for example easily to all CDS). Maybe this could save you some work. ...
written 7.2 years ago by skymningen330
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Comment: C: Isn'T A Prokaryotic Gene Continuous..?
... I just looked up, what is in the space included. (In this case, transposes.) This often gives you an idea. Functional genes in procaryotes shouldn't be interrupted, though. ...
written 7.2 years ago by skymningen330
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Answer: A: Isn'T A Prokaryotic Gene Continuous..?
... The gene in your link is only a pseudogene, that has been interrupted by transposases. (Gene on NCBI) In this (or similar) cases, also a procaryotic gene without introns can be joint from several locations. ...
written 7.2 years ago by skymningen330
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Answer: A: Database Of Cultured Bacterial 16S Rdna Sequences
... At the Ribosomal Database project, you can browse for (and download) only isolates. ...
written 7.2 years ago by skymningen330
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Comment: C: Getting Error In Bowtie2
... Did you check if it runs with just bowtie2 -q --phred33 -x targreads -U In_file.fastq -S out_file.sam ? Then all you need is adding the other parameters one by one and check from what parameter your error comes from. ...
written 7.3 years ago by skymningen330
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Comment: C: Mauve Contig Mover
... The contig mover only uses the normal progressive_mauve command. It is no singular tool, but uses iterative runs of progressive_mauve (or the old mauve, I am not completely sure) to get the contig order that includes the least rearrangements in comparison to the reference. Edit: What I meant to say ...
written 7.3 years ago by skymningen330
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Answer: A: Getting Error In Bowtie2
... I think there are several problems. First, like matted said, you miss some parameter values. Second, I am not sure you got the right input for -x as well. So there's what you did: bowtie2 -q --phred33 -x targreads -U -S --un --no-unal --rg-id --rg I'll be speculating on some things you might hav ...
written 7.3 years ago by skymningen330

Latest awards to skymningen

Popular Question 6.1 years ago, created a question with more than 1,000 views. For Bcftools Back And Forth Conversion Error
Supporter 6.5 years ago, voted at least 25 times.
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Isn'T A Prokaryotic Gene Continuous..?
Teacher 7.2 years ago, created an answer with at least 3 up-votes. For A: Database Of Cultured Bacterial 16S Rdna Sequences
Good Answer 7.4 years ago, created an answer that was upvoted at least 5 times. For A: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Teacher 7.4 years ago, created an answer with at least 3 up-votes. For A: Are We Rude/Do We Expect Too Much From People Asking Questions On This Forum?
Teacher 7.7 years ago, created an answer with at least 3 up-votes. For A: A Farewell To Bioinformatics

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