User: am3

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am370
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Posts by am3

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Tutorials for forging BSGenome packages?
... Lots of Bioconductor packages require a BSGenome data package to work, but they're only available for a limited number of organisms, so as far as I understand, if you work on one that's not available you're supposed to "forge" a BSGenome package of your genome yourself. I find the [official vignett ...
genome R bioconductor written 6 months ago by am370
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Answer: A: Tophat vs Bowtie alignment rates
... Hi everyone, I have an answer to this after consulting with one of the developers. Posting in case anyone here is interested or comes across this when googling. The difference between how Bowtie2 runs by default and how Tophat2 calls Bowtie2 is in the minimum alignment score required to consider an ...
written 8 months ago by am370
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Comment: C: Tophat vs Bowtie alignment rates
... I would think that things like polyAs or other generally problematic sequences would be equally problematic in Bowtie and Tophat, no? Unless when Tophat calls Bowtie it calls it using some setting that drastically changes how such reads are treated (which is what I haven't been able to figure out). ...
written 8 months ago by am370
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Comment: C: Tophat vs Bowtie alignment rates
... Good questions - the reads are paired-end and have been trimmed and QC'ed. The reports say that of the reads that do map, most map concordantly, so I don't think there's anything weird going on with how it's treating the pairs, but I'm not sure what else I should check. ...
written 8 months ago by am370
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Comment: C: Tophat vs Bowtie alignment rates
... With genuine thanks to everyone here for taking the time to answer, I'd like to gently suggest that we move away from discussion of the "best" tools in some global sense. I'm not looking for advice on how to do my final analysis. As I explained, I'm motivated by curiosity. My goal in THIS instance i ...
written 8 months ago by am370
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Comment: C: Tophat vs Bowtie alignment rates
... Thank you! I do indeed mean Tophat2. The manual just calls it Tophat (whereas the manuals for bowtie2 calls it bowtie2 every time), which is why I was imprecise. I thought the issue might be local vs. end-to-end, however the bowtie2 manual says it does end-to-end by default: http://bowtie-bio.sour ...
written 8 months ago by am370
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Comment: A: Tophat vs Bowtie alignment rates
... Thank you, I'm aware of the improved methods that exist, but I'm asking the question to satisfy my curiosity now, to better understand both my data and the methods. According to the manual, Tophat indeed uses bowtie2: https://ccb.jhu.edu/software/tophat/manual.shtml, so I don't think that's it. I ...
written 8 months ago by am370
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Tophat vs Bowtie alignment rates
... Hello! I hope somebody can provide some insight into TopHat and Bowtie2 behavior. I have a data set that I aligned to a reference using Bowtie2 and Tophat, both running default settings. When I used Bowtie, the alignment rates were >90% for all samples. With Tophat, however, the rates were all ar ...
bowtie2 tophat alignment written 8 months ago by am370
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Understanding Bowtie output
... Hello, I'm using bowtie2 to align some whole-exome sequencing reads and have a basic question about the output I get. The summary text includes the line `X% aligned concordantly >1 times.` In my files, X is generally pretty high (40% or so). However, I did not specify `-k` or `-a` when I ran t ...
alignment bowtie written 9 months ago by am370 • updated 9 months ago by manuel.belmadani1.1k

Latest awards to am3

Appreciated 8 months ago, created a post with more than 5 votes. For A: Tophat vs Bowtie alignment rates
Scholar 8 months ago, created an answer that has been accepted. For A: Tophat vs Bowtie alignment rates
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Tophat vs Bowtie alignment rates

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