User: dariober

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dariober7.5k
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Posts by dariober

<prev • 645 results • page 1 of 65 • next >
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Answer: A: Malformed VCF file at approximately line number 101449: The VCF specification d
... Philipp Bayer's solution is good but since the error says "approximately at line number ...", the offending line maybe somewhere else. Also there might be other buggy lines. This awk script will print lines where the 8th field contains a space and it will print the line number as well: awk -v ...
written 20 hours ago by dariober7.5k
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Comment: C: Codon change from HGVS.c notation
... Loosely related... [VEP][1] can be run as a standalone program with a local database so if you have lots of data you don't have do go through their server. [1]: http://www.ensembl.org/info/docs/tools/vep/script/index.html ...
written 3 days ago by dariober7.5k
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Comment: C: Parsing gff files using python and awk
... I think `FS= "{\t ;:}"` will not compile, it should be `-F"[\t ;:]"` or `-v FS="[\t ;:]"` (I don't know if your script will do what you expect after this). Also, if you use awk you assume that each line has the same number of fields in the same order. This is fine for the first 8 columns of the gtf ...
written 5 days ago by dariober7.5k
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Comment: C: Survey: What colour theme do you use in your terminal?
... Thank you. Yes, I'm under the impression that the dark background, whether black or solarised, is more popular than the light one. ...
written 6 days ago by dariober7.5k
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Comment: C: Survey: What colour theme do you use in your terminal?
... Hi- Thanks for your feedback! With the version I uploaded just today, 1.3.0, the user can choose one of the three built-in themes or upload a configuration of their choice through a file based on these [templates][1]. About font, ASCIIGenome simply uses the font you run on your terminal so you can ...
written 7 days ago by dariober7.5k
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6 follow
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Survey: What colour theme do you use in your terminal?
... In my pet project, [ASCIIGenome][1] a genome browser for terminals, I would like to support more colour themes. To make ASCIIGenome match your preferences, I would like to get an idea of what colors you guys typically choose for your terminals. It would be great if you could post here either a desc ...
theme terminal color written 7 days ago by dariober7.5k • updated 6 days ago by jrj.healey800
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Comment: C: Deciding on a Variant Caller
... In fact I was hoping for a reference other than the authors' paper... ...
written 11 days ago by dariober7.5k
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Comment: C: Deciding on a Variant Caller
... > MuSE outperforms MuTect2 Do you have a reference for this statement (I'm genuinely interested I don't mean to argue for or against it) ...
written 12 days ago by dariober7.5k
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Comment: C: How do you perform functional testing for your Bioinformatics tools?
... Interesting topic... But I personally disagree with Istvan. I cannot claim either a long or deep experience but I found test-driven development (test-first philosophy) good. It took (actually it's taking) me a while to get my head around it but [this book][1] was very useful. By writing tests firs ...
written 14 days ago by dariober7.5k
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Comment: C: What is the limiting factor for trimmomatic speed and how can it be increased?
... I was going to suggest slicing the input fastq's. However, the slicing & merging makes the whole processing more complicated and error prone and I wonder if it's worth. If time is crucial I would consider also/instead piping the output of the trimmer to the aligner. I put simple howto here https ...
written 16 days ago by dariober7.5k

Latest awards to dariober

Teacher 9 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 14 days ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Picard API: Modify sam header
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Output the color code according to number
Good Question 10 weeks ago, asked a question that was upvoted at least 5 times. For When and why is bwa aln better then bwa mem?
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Output the color code according to number
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 3 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 3 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 5 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Appreciated 5 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Popular Question 5 months ago, created a question with more than 1,000 views. For markDuplicates: Histogram not produced
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For When and why is bwa aln better then bwa mem?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites

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