Moderator: dariober

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Posts by dariober

<prev • 814 results • page 1 of 82 • next >
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Comment: C: How to write the output in snakefile (snakemake) for bowtie2-build
... The shell command is executed but it is throwing an error. In fact, `bowtie2-build` should have two positional arguments but there's only one: bowtie2-build /home/s1104230/mapping2/reference It should be something like: bowtie2-build /home/bnextgen/refgenome/infected_consensus.fasta /h ...
written 15 hours ago by dariober9.5k
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Answer: A: How to write the output in snakefile (snakemake) for bowtie2-build
... IP's answer is what I would do. An alternative is to use the `touch` function to create a marker file that signals that a task has successfully completed: rule bowtie2Build: input: "/home/bnextgen/refgenome/infected_consensus.fasta" params: basename: "/home/s1104230/ ...
written 3 days ago by dariober9.5k
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Answer: A: Error in cutadapt installation
... See if this Q&A on stack overlflow helps https://stackoverflow.com/questions/25981703/pip-install-fails-with-connection-error-ssl-certificate-verify-failed-certi According to the top answer you may just need to add flags `--trusted-host pypi.org --trusted-host files.pythonhosted.org` to your pi ...
written 7 days ago by dariober9.5k
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Comment: C: Is BED file generated by bametobed sorted ?
... I don't think you need to convert BAM to BED in order to take advantage of the `-sorted` option of coverageBed. Just pass the bam file to `-a` with the `-sorted`and possibly the `-g` option enabled. Anyway, I would guess the conversion BAM to BED doesn't change the order of records so if your BAM ...
written 12 days ago by dariober9.5k
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Answer: A: giving a color to null values on heatmap2
... I haven't tried it, but [heatmap.2][1] takes the argument `na.color` which should suite you: *Color to use for missing value (NA). Defaults to the plot background color.* (How can you have missed it? heatmap.2 takes only 59 arguments!) [1]: https://www.rdocumentation.org/packages/gplots/versions ...
written 16 days ago by dariober9.5k
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Comment: C: Alternative to VEP.
... +1. I would make this comment an answer. Besides, VEP can be run on multiple cores and it doesn't take long to annotate hundreds of thousands of variants. ...
written 18 days ago by dariober9.5k
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Comment: C: Organizing tools/ software
... Hi- I'm not very familiar with docker and friends (they have been on my todo list for quite a while...). Are you suggesting that every time you start a new project you should create a docker instance with all the necessary tools in it (like bwa, bedtools, R & packages, custom scripts etc)? Then ...
written 22 days ago by dariober9.5k
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Answer: A: clonal populations in cancer samples
... In addition to Kevin's answer, [Quantification of subclonal selection in cancer from bulk sequencing data][1] and references therein may be another useful read. If you want some sensible cutoff for some rough analysis or filtering, I would say 20% AF is about right, but again, as Kevin says it depe ...
written 24 days ago by dariober9.5k
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Comment: C: Why do R1 and R2 compressed files have different size
... >One might have sequences that are a little more repetitive Mmm... The difference the OP observes is quite noticeable. If the sequence is the cause, it may indicate some problem as read1's and read2's should be pretty random with respect to the genomic position. See my answer below for an altern ...
written 4 weeks ago by dariober9.5k
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Answer: A: Why do R1 and R2 compressed files have different size
... A wild guess... Second-in-pair reads usually have base qualities that drops faster along the read compared to first-in-pair. This makes the quality line on each fastq record more variable (i.e. more random and less compressible) in R2 than in R1. ...
written 4 weeks ago by dariober9.5k

Latest awards to dariober

Scholar 12 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 14 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 24 days ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 24 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 4 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Scholar 6 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Scholar 7 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Popular Question 8 weeks ago, created a question with more than 1,000 views. For Inconsistent GTF from UCSC browser vs genePredToGtf
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Popular Question 12 weeks ago, created a question with more than 1,000 views. For Expected number of read duplicates
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
Scholar 4 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 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
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
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
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: Filtration Of Reads With Length Lower Than 30 From Bam
Scholar 7 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 7 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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