Moderator: dariober
dariober ♦ 9.5k
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Posts by dariober
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... 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
dariober ♦ 9.5k
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... 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
dariober ♦ 9.5k
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... 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
dariober ♦ 9.5k
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... 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
dariober ♦ 9.5k
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... 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
dariober ♦ 9.5k
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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
dariober ♦ 9.5k
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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
dariober ♦ 9.5k
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... 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
dariober ♦ 9.5k
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... >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
dariober ♦ 9.5k
2
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... 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
dariober ♦ 9.5k
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