Moderator: dariober
dariober ♦ 11k
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Posts by dariober
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... If I understand correctly, I would make `path_to_bams.txt` a table that links input files to sample names, like this:
sample infile
s1 path/to/a.bam
s2 path/to/b.bam
s3 path/to/c.bam
Then read this file in a pandas dataframe and use a lambda function to assign t ...
written 7 days ago by
dariober ♦ 11k
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... Can you provide an example of alignments you want to keep and examples that you want to filter out? ...
written 17 days ago by
dariober ♦ 11k
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... See also this thread https://www.biostars.org/p/95700/ I suggested there [pysamstats](https://github.com/alimanfoo/pysamstats) and I'm still quite happy with it. ...
written 18 days ago by
dariober ♦ 11k
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... > What can i do to avoid reads that can find multiple perfectly matches
If by that you mean to filter out reads that map equally well to multiple locations, then you should filter by MAPQ score in the alignment file, e.g. `samtools view -b -q 5 in.bam > out.bam`. The exact MAPQ threshold you ...
written 18 days ago by
dariober ♦ 11k
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Comment:
C: Using R Studio on Cloud
... > Why don't you connect to the HPC with X11-forwarding and then run RStudio on the HPC?
That could work but in my experience the X11-forwarding is painfully slow (that's why I wrote this [genome browser](https://asciigenome.readthedocs.io/en/latest/)). I use R a LOT and virtually all of it on re ...
written 6 weeks ago by
dariober ♦ 11k
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... I agree that, depending on volume of data and turnaround time, doing NGS analysis on a desktop is possible these days. However, I find your comparison with HPC a bit misleading as I'm not sure that a single server with 40 CPUs can be considered a "high performance cluster" (by the way, what does C s ...
written 6 weeks ago by
dariober ♦ 11k
0
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... To fix the issue with margins I think you have to play with the `attribute.plots` parameter and `theme(plot.margin = unit(c(...), "cm")))` (see examples in `?upset`). I think @Papyrus is correct about `nintersects` (+1, why not making it an answer?) ...
written 7 weeks ago by
dariober ♦ 11k
2
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1
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152
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Answer:
A: I can/t use mkdir -p ~/bin
... Here's my guess (I don't have a MacOS to test). There is already a file `/Users/apple/bin` (a file, not a directory) so when you try to make a directory called `bin` in `/Users/apple` mkdir fails even if you have `-p` because you can't replace the file with a directory. I don't know why the comments ...
written 7 weeks ago by
dariober ♦ 11k
0
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... Thanks for this. `conda install 'meme=5.0.2' 'icu=58.2'` may be more explicit than `conda install bioconda/label/cf201901 meme` ...
written 7 weeks ago by
dariober ♦ 11k
0
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1
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373
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... I also got this error with hisat2 v2.2.0 but v2.1.0 works fine. Must be a recent change...? ...
written 8 weeks ago by
dariober ♦ 11k
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For A: Visualize reads in BAM file
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For A: Output the color code according to number
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For A: Visualize reads in BAM file
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For A: Visualize reads in BAM file
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For A: Visualize reads in BAM file
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For A: Replace fields CHROM and POS in a vcf file
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For A: Replace fields CHROM and POS in a vcf file
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For A: plotting interactions in R with two data sets
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