Moderator: dariober

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dariober10k
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Posts by dariober

<prev • 853 results • page 1 of 86 • next >
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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 8 days ago by dariober10k
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Answer: A: estimate tumor purity from target capture sequencing
... 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 dariober10k
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Comment: C: How To Efficiently Sort A Fastq File By Entry Id?
... 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 dariober10k
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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 dariober10k
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Mutate protein sequence according to HGVS
... 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...). ...
hgvs fasta protein written 3 months ago by dariober10k • updated 3 months ago by Emily_Ensembl19k
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Comment: C: Samtools view -f "OR" operator possible?
... 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 dariober10k
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Answer: A: Samtools view -f "OR" operator possible?
... 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 dariober10k
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Answer: A: Automating the creation of IGV style histogram coverage maps
... 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 dariober10k
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Comment: C: biojava get qualityscores of sequence
... 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 dariober10k
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Answer: A: biojava get qualityscores of sequence
... 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 dariober10k

Latest awards to dariober

Scholar 19 days ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
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Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Scholar 10 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Output the color code according to number
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Scholar 5 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 5 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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Appreciated 10 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Popular Question 11 months ago, created a question with more than 1,000 views. For Computational Biologist - Cambridge University/CRUK
Scholar 11 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Popular Question 11 months ago, created a question with more than 1,000 views. For Computational Biologist - Cambridge University/CRUK
Teacher 11 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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