Moderator: dariober
dariober ♦ 10k
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Posts by dariober
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... 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 8 days ago by
dariober ♦ 10k
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... The [facets](https://github.com/mskcc/facets) package detects copy number variants and gives you the purity and ploidy estimates.
If interested, I also wrote a wrapper to run the analysis as a single line command, see [cnv_facets](https://github.com/dariober/cnv_facets). ...
written 9 weeks ago by
dariober ♦ 10k
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... Hi Chetana- It may be that there is a tab instead of a backspace between the read name (`@M00189:187:000000000-CK2YF:1:1101:10001:13101`) and the `1:N:0:1` part. You can check with e.g. `zcat my.fastq.gz | grep -P '\t' | head` (which should print nothing if there is no tab).
If you do a have a tab ...
written 9 weeks ago by
dariober ♦ 10k
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Comment:
C: How to get my tool on Homebrew ?
... Maybe too late, maybe irrelevant... But have you considered submitting your program to [bioconda](https://bioconda.github.io/index.html) instead? I think (bio)conda is more popular than homebrew in bioinformatics and the users of your program get the benefits of the conda ecosystem like separate env ...
written 3 months ago by
dariober ♦ 10k
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... Hi- Before I reinvent the wheel... I need to modify a set of reference protein sequences in fasta format according to given variants in [HGVS format](http://varnomen.hgvs.org/).
Can you suggest any tool or package to do it? A Python package would be best but any would do (R, Java, standalone...). ...
written 3 months ago by
dariober ♦ 10k
• updated
3 months ago by
Emily_Ensembl ♦ 19k
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... Maybe worth noting that this will output duplicate alignments if a record matches more than one OR conditions (e.g. for 2052 which is not really possible in this case but you never know...) ...
written 3 months ago by
dariober ♦ 10k
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... The closest I can think of is, using samtools (not tested):
samtools merge - \
<(samtools view -u -f 4 in.bam) \
<(samtools view -u -f 2048 in.bam)
This will output BAM to stdout, replace `-` with an actual output filename. ...
written 3 months ago by
dariober ♦ 10k
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... If you are ok with R, have a look at [Gviz](https://bioconductor.org/packages/release/bioc/html/Gviz.html). For something scriptable but with not very polished output see [ASCIIGenome](https://asciigenome.readthedocs.io/en/latest/description.html) (disclaimer- I'm the author) ...
written 3 months ago by
dariober ♦ 10k
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... See edit... Basically, convert ASCII to decimal and from there to quality score using the appropriate offset. Here I use -33 to produce Sanger scores. I don't think it is possible to always decide unambiguously, i.e. automatically, what offset should be used although after reading a few sequencing o ...
written 4 months ago by
dariober ♦ 10k
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... Maybe you are making things more complicated than they need in your code. Wouldn't this work?
FastqReader fastqReader = new SangerFastqReader();
File in = new File("fastqfile.fastq");
fastqReader.read(in);
for (Fastq fastq : fastqReader.read(in)) {
String qual = fastq.getQu ...
written 4 months ago by
dariober ♦ 10k
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