User: dariober

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Posts by dariober

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Comment: C: How To Efficiently Sort A Fastq File By Entry Id?
... Hi- If you want `xxxx.10` to come after `xxxx.2`, use the `--V/--version-sort` option in the sort command. ...
written 1 day ago by dariober7.5k
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Comment: C: why dont we need technical replicate in case of RNA Seq.?
... I would like to link my answer to https://www.biostars.org/p/149538/ about the distinction (or lack thereof) between what are "technical" and "biological" replicates. ...
written 3 days ago by dariober7.5k
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Comment: C: Downsample BAM file
... (...I was impressed by the speed of writing of Pierre, not of the script!) If you want a coverage of exactly 1x (or zero if there are no reads in a region) then I think you need something else then Pierre's script. For each position his script gives one read *starting* there, which is not going to ...
written 18 days ago by dariober7.5k
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Comment: C: Downsample BAM file
... That's great (if not anything else for the speed of writing it!). But if I understand your script it correctly, Pierre, you are picking one read from multiple ones *starting* at the same position. My understanding of the question is to have, essentially, a BAM file with depth of coverage of exactly ...
written 18 days ago by dariober7.5k
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Answer: A: What is a gene transcript?
... This is more of a comment, possibly a rant. In my opinion the concept of gene is obsolete and we would be better off if we ditched the concept of "gene" altogether. Genes made sense when it was thought that there were these discrete units (genes) which produced each a single transcript and a singl ...
written 25 days ago by dariober7.5k
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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 4 weeks 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 4 weeks 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 weeks 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 5 weeks 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 5 weeks ago by dariober7.5k

Latest awards to dariober

Popular Question 5 days ago, created a question with more than 1,000 views. For Java Samtools Api: Write Bam To Stdout
Teacher 20 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 29 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Picard API: Modify sam header
Teacher 10 weeks 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
Good Question 3 months ago, asked a question that was upvoted at least 5 times. For When and why is bwa aln better then bwa mem?
Appreciated 3 months ago, created a post with more than 5 votes. For A: Output the color code according to number
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 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 4 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 4 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 6 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 6 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets

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