User: d-cameron
d-cameron • 1.9k
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Posts by d-cameron
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... > gns <- genes(TxDb.Hsapiens.UCSC.hg19.knownGene)
genes(hg19) returns some really strange results. You'll want to use transcripts() instead as some genes are annotated have two transcripts 100+Mb apart so genes() matches almost the whole chromosome for those.
The clinical pipelines I'm invol ...
written 3 months ago by
d-cameron • 1.9k
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... This question is actually very well timed. The GAG4H file formats working group has an upcoming teleconference on the future of VCF and a potential new file format. I strongly recommend getting involved if there are limitations in the existing file formats that make it unsuitable for your use case. ...
written 3 months ago by
d-cameron • 1.9k
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... You have redirected the bwa standard error output stream (stderr) to the same location as the standard output stream (stdout. Check your bwa command as redirects such as `2>&1` will do this.
Check your shell configuration as well as some configurations will perform this redirect automaticall ...
written 4 months ago by
d-cameron • 1.9k
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... No matter what compressed storage format you use, the majority of the entropy in sequence data is actually in base quality scores, not the actual sequences. If you want 50%+ improvement over fq.gz then you'll be forced to discard information - base quality score binning will make a bigger difference ...
written 4 months ago by
d-cameron • 1.9k
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... >it can clip bases, you'll want to relax the defaults
The bases are soft clipped so the information is still there. Only supplementary alignments are hard clipped but the information is in the primary alignment anyway.
>reads could also be filtered if they don't map to the reference genome
...
written 4 months ago by
d-cameron • 1.9k
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Comment:
C: How to run IGV
... Run igv.bat from a command prompt to see the error message. ...
written 4 months ago by
d-cameron • 1.9k
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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 4 months ago by
d-cameron • 1.9k
0
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1
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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 4 months ago by
d-cameron • 1.9k
2
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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 4 months ago by
d-cameron • 1.9k
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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 4 months ago by
d-cameron • 1.9k
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