User: d-cameron
d-cameron • 1.8k
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Posts by d-cameron
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... I just use -X 1000 so it works on practically all input libraries. Aren't you getting fewer concordantly alignment reads now? Check the documentation on your simulator (and run picard CollectionInsertSizeMetrics) to see what fragment lengths you've actually simulated.
The community can't agree on w ...
written 14 hours ago by
d-cameron • 1.8k
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... Unless you've given a custom -X parameter to bowtie2, fragments longer than 500bp are going to be considered discordant. ...
written 18 hours ago by
d-cameron • 1.8k
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... > See one of my alignment information as below, although it has 100% overall alignment, what is wrong with '1670714 (97.50%) aligned concordantly 0 times'?
Nothing is wrong per se, it's just a combination of bowtie2 incorrectly placed at least one of the reads and/or the fragment size being unus ...
written 19 hours ago by
d-cameron • 1.8k
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... > what is the optimal strategy to connect these pairs of letters into a sequence
Typically assembler are looking for a [Eulerian path][1], Hamiltonian cycle, or a variation of one of those approaches.
[1]: https://en.wikipedia.org/wiki/Eulerian_path ...
written 19 hours ago by
d-cameron • 1.8k
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... >are these two totally different quality checks?
These are two totally different quality checks.
Mark duplicates removes fragments that been sequenced multiple times due to PCR amplification.
MAPQ filtering removes reads that are ambiguously placed by the aligner. When a read aligner places a ...
written 2 days ago by
d-cameron • 1.8k
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... This can be solved by qualifying the path to your picard.jar file. For example, if you have downloaded picard.jar to the bin subdirectory of your home directory, you would change your command line to. `java -jar $HOME/bin/picard.jar` ...
written 5 days ago by
d-cameron • 1.8k
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... What do you want to happen when you reach 100 Ns in a row? ...
written 6 days ago by
d-cameron • 1.8k
1
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... >I am getting good results, but the sensitivity is not that great.
How do you know this? How dissimilar do your sequences need to be before you consider a hit to be a false positive?
>I have set of subject sequences (25 to 40 bps long). My query sequences are 200-300 bp long. I have tried bo ...
written 10 days ago by
d-cameron • 1.8k
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... > Is it the case that it would look like both "...ATGT G CTGA..." and "...ATGT T CTGA..." ? and is there a way in which I can determine which is the "correct" sequence to use?
For germline human sequencing, both are correct because each person has two copies of each autosomal gene.
It's even mo ...
written 18 days ago by
d-cameron • 1.8k
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... > I'm thinking of using R package like dplyr to group by coordinates, but for so many files with so many lines, it may not be efficient.
50 million records isn't that big a data set. How many zeros are you expecting once you `spread()` you data into a matrix?
...
written 22 days ago by
d-cameron • 1.8k
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