Moderator: dariober

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dariober11k
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Posts by dariober

<prev • 912 results • page 1 of 92 • next >
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Comment: C: How to extract reads with no INDEL?
... @shimbalama - If you really wanted to you could write an awk script that parses the cigar string and checks for a D operator > 20. But I think it would be easier to write a python script using the pysam package to parse the cigar string or see if Pierre's tools can do it (probably they can). If y ...
written 1 day ago by dariober11k
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Comment: C: How to open HUGE excel files with genomic info
... The geeky detail is that I use the Java [POI package](https://poi.apache.org/) which, it seems to me, is way more sophisticated than various python/R counterparts and gives a lot of low-level options to manipulate cells. In general, it seems to do "the right thing". But basically, by default my prog ...
written 28 days ago by dariober11k
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Comment: C: How to open HUGE excel files with genomic info
... I kind of advise against pandas for this. For example, see this question of mine on [stackoverflow](https://stackoverflow.com/questions/60802014/how-to-consistently-handle-excel-boolean-with-pandas). In general, I *think* pandas and R-based solutions don't handle well input that is not already nicel ...
written 28 days ago by dariober11k
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Answer: A: How to open HUGE excel files with genomic info
... It seems Excel has a limit of [1,048,576 rows](https://support.microsoft.com/en-us/office/excel-specifications-and-limits-1672b34d-7043-467e-8e27-269d656771c3) so I suppose your SNPs are split across different sheets. If any useful, I wrote an [excelToCsv](https://github.com/dariober/excelToCsv) co ...
written 29 days ago by dariober11k
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Answer: A: Centrimo error: Template does not contain data section
... If any useful, this is how I installed the latest meme (5.3.0) using a mixture of conda and source code * Create a conda environment with these dependencies: - python >=3.0 - perl =5.22.0.1 - zlib - ghostscript - perl-xml-parser - perl-yaml ...
written 4 weeks ago by dariober11k
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Comment: C: Is there a reasonable way to rank peaks that are common between replicates?
... Man, I've been facing this question so many times and I still don't have a satisfying answer. ...
written 5 weeks ago by dariober11k
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Answer: A: Can I use Negative Binomial regression to model TPM counts?
... After log transformation, TPMs should follow fairly well a normal distribution so you may just use standard linear regression. I don't think negative binomial would be a good choice as it is best suited to count data. Maybe a GLM with gamma distribution would be more appropriate. Alternatively, I wo ...
written 10 weeks ago by dariober11k
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Comment: C: BWA mem minimum read length
... If you can upload a representative sample of reads, say a few hundred thousand, to e.g. dropbox along with the reference genome (either the genome itself or a link to it) maybe some of us can take a look at the issue. ...
written 10 weeks ago by dariober11k
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Comment: C: fastq-dump returns I1 and R1 files instead of R1 and R2
... I got curious and I looked up [SRR8712342](https://www.ebi.ac.uk/ena/browser/view/SRR8712342) on ENA archive. It looks there is only 1 fastq file there even if the run is paired-end. All reads have length 98bp and read names all end with "/2" which (sometimes) means read 2. Odd... I don't know if it ...
written 10 weeks ago by dariober11k
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Comment: C: EdgeR exactTest help
... It seems to me that you are simulating 1 gene and 10000 samples, is that what you really want? It's an extremely unusual situation. ...
written 10 weeks ago by dariober11k

Latest awards to dariober

Popular Question 27 days ago, created a question with more than 1,000 views. For Computational Biologist - Cambridge University/CRUK
Epic Question 27 days ago, created a question with more than 10,000 views. For When and why is bwa aln better then bwa mem?
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Appreciated 8 weeks ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
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Scholar 12 weeks ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Scholar 3 months ago, created an answer that has been accepted. For A: Visualize reads in BAM file
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Scholar 4 months ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: count the number of transcription factor binding sites
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
Popular Question 7 months ago, created a question with more than 1,000 views. For Computational Biologist - Cambridge University/CRUK
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
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Scholar 8 months ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Appreciated 8 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Scholar 9 months ago, created an answer that has been accepted. For A: Visualize reads in BAM file
Appreciated 10 months ago, created a post with more than 5 votes. For A: Output the color code according to number
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file
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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
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Visualize reads in BAM file

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