Moderator: dariober
dariober ♦ 11k
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Posts by dariober
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... @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
dariober ♦ 11k
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... 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
dariober ♦ 11k
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... 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
dariober ♦ 11k
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... 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
dariober ♦ 11k
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... 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
dariober ♦ 11k
0
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... Man, I've been facing this question so many times and I still don't have a satisfying answer. ...
written 5 weeks ago by
dariober ♦ 11k
2
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233
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... 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
dariober ♦ 11k
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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
dariober ♦ 11k
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... 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
dariober ♦ 11k
0
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1
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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
dariober ♦ 11k
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For A: count the number of transcription factor binding sites
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