Moderator: dariober

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dariober10k
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Posts by dariober

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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 9 days 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 weeks 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 weeks ago by dariober10k
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Answer: A: bedops bedmap operation in python
... Hi- I'm not sure if there is a python API for bedops (similar to pybedtools, if this is what you mean). However, in a python script you can use the [subprocess][1] library to execute external commands. E.g. something like (see also [check_call](https://docs.python.org/3/library/subprocess.html#subpr ...
written 8 weeks ago by dariober10k
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Answer: A: How to visualize bam, bed and vcf files programmatically using Python and Shell
... Assuming that by "visualize" you mean showing coverage and/or alignments in genomic windows, you can use [Gviz](http://bioconductor.org/packages/release/bioc/html/Gviz.html) if you are ok with R. For quick, explorative visualization directly from the command line I wrote [ASCIIGenome](https://asciig ...
written 10 weeks ago by dariober10k
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Comment: C: How do Read Alignment tools detect PCR duplicates?
... Keep in mind also that the label "PCR duplicate" is a bit misleading. In fact, it refers to positional duplicates, i.e. reads or read pairs with identical alignment coordinates. As far as I know, in typical Illumina sequencing libraries there is no way to tell apart positional duplicates from PCR du ...
written 3 months ago by dariober10k
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Answer: A: How to find the promotor region of a given gene by using IGV
... As far as I know, promoters are still very loosely defined as the regulatory region upstream of a gene, usually 1kb upstream (things are further complicated by the fact that you have multiple transcripts per gene). So to find a promoter in IGV just go to the transcript start site of your gene and pi ...
written 3 months ago by dariober10k
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Comment: C: How do BWA and Bowtie2 decide where to place paired reads and what flags affect
... Sometimes these sort of questions is best answered by preparing some test cases and see what happens. For example, write a dummy genome of 1000bp with some repeats, write a pair of fastq files with a handful of reads mapping to or near the repeats, index, align and see the results. (In theory, a con ...
written 3 months ago by dariober10k
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Comment: C: MACS2 option for ATAC seq?
... Hi- My 2p, I just started using [Genrich][1] on ATAC-seq with replicates and my first impression is actually very good when comparing it to MACS2 (I may post a better explanation at some point...). [1]: https://github.com/jsh58/Genrich ...
written 3 months ago by dariober10k
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Answer: A: Bash script iterating over 2 arrays
... I don't know exactly what's happening with your command but I think to create the arrays you can use something like array=(`ls -1 /Users/personal/Desktop/blackberry_hybseq_data/Data_and_Nov2018_NZ_assembly/blackberry_hybseq/*gz`) Then iterate with: for ((i=0; i<${#array[@]}; ++i)); ...
written 4 months ago by dariober10k

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Appreciated 8 days ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
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Scholar 6 weeks ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
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Popular Question 7 months ago, created a question with more than 1,000 views. For Computational Biologist - Cambridge University/CRUK
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
Popular Question 7 months ago, created a question with more than 1,000 views. For Computational Biologist - Cambridge University/CRUK
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Teacher 8 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Scholar 8 months ago, created an answer that has been accepted. For A: Replace fields CHROM and POS in a vcf file
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: plotting interactions in R with two data sets
Appreciated 9 months ago, created a post with more than 5 votes. For A: Output the color code according to number

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