Moderator: dariober

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dariober11k
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WCIP | Glasgow | UK
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7 years, 5 months ago
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Posts by dariober

<prev • 862 results • page 1 of 87 • next >
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Answer: A: Snakemake and BBsplit.sh for filtrate human reads : memory management
... I think you can use the [resources](https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#resources) directive in combination with the `--resources` command line option. E.g., your rule `clen_fastq` could be: rule clean_fastq: resources: mem_gb= 20, ...
written 5 weeks ago by dariober11k
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Answer: A: Which genome browser to use for my data?
... Thanks for sharing! Partly as a shameless plug... I wrote [ASCIIGenome](https://asciigenome.readthedocs.io/en/latest/description.html) because it covers a need that none of the others satisfies: It runs on the terminal without graphical interface. Since I work almost exclusively on remote servers, a ...
written 11 weeks ago by dariober11k
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Comment: C: FASTQ Phred33 average base quality score
... Two years later... +1! I spent the last 2 hours trying to figure out why my dumb average of phred scores didn't match NanoPlot's (+1 also to that) until I dug into its code and eventually found this thread. ...
written 12 weeks ago by dariober11k
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Answer: A: How to read vcf.bgz or vcf.gz in python using PyVcf?
... I haven't tried it by I think you should use the `filename` parameter: vcf_reader = vcf.Reader(filename='input.vcf.gz') ...
written 3 months ago by dariober11k
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Comment: C: Bioinformatics vs. the Climate Crisis
... > There is no climate crisis Are you saying that the climate is not changing or that the change is not a big deal? Either way, this is a difficult position to hold as there is tons of scientific research supporting the case of the climate crisis. ...
written 4 months ago by dariober11k
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Comment: C: Interpretation of RNA seq pipeline in a paper
... You are right, well spotted - I corrected my answer ...
written 4 months ago by dariober11k
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Answer: A: Interpretation of RNA seq pipeline in a paper
... Granted that mine is a guess since I haven't read the paper... > the authors have somehow integrated RPKM along with the edgeR package Mmm... no, I don't think so... They used edgeR for detecting differentially expressed genes and they considered as biologically relevant genes with FDR < 0.0 ...
written 4 months ago by dariober11k
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Comment: C: Job management programs
... Hi Devon, would you mind expanding on that? I mean, I know you can install slurm on a single node, but is it something reasonably doable by someone without admin rights and without investing a fair bit of effort maintaining slurm over time? ...
written 4 months ago by dariober11k
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Answer: A: Job management programs
... Depending on how much effort you want to invest, you could run your program(s) via [snakemake](https://snakemake.readthedocs.io/en/stable/) and let snakemake handle parallelism and job dependencies. There will be a learning curve but in my opionion is totally worth it. Alternatively, with `xargs` ( ...
written 4 months ago by dariober11k
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Answer: A: RNA-Seq minimum read length recommendations
... Hi- For a discussion about adapter trimming you may find this thread useful https://www.biostars.org/p/212136/ > there doesn't seem to be such a clear consensus on a good minimum read length except to say that overly short reads can cause spurious alignment Spurious alignments should have zero ...
written 6 months ago by dariober11k

Latest awards to dariober

Scholar 10 days ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Appreciated 17 days ago, created a post with more than 5 votes. For A: Output the color code according to number
Scholar 4 weeks ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Teacher 7 weeks ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Appreciated 3 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Prophet 3 months ago, created a post with more than 20 followers. For ChIP-Seq: Calling peaks with replicates
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: Adapter trimming tool for Windows?
Good Answer 4 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Scholar 4 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Appreciated 4 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Popular Question 4 months ago, created a question with more than 1,000 views. For Computational Biologist - Cambridge University/CRUK
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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Good Answer 8 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Scholar 8 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Appreciated 8 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Appreciated 9 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Teacher 10 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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