Moderator: JC
JC ♦ 10k
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Computational Biologist
Posts by JC
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Answer:
A: VEP cache trancript versions
... > Why VEP does not use use the same GFF file ?
They can't, both reference genomes are not the same, so the annotation and coordinates in some regions are different ...
written 4 days ago by
JC ♦ 10k
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... The UCSC Genome Browser provides the genome with repeats masked in this file http://hgdownload.soe.ucsc.edu/goldenPath/mm10/bigZips/chromFaMasked.tar.gz ...
written 5 days ago by
JC ♦ 10k
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... Yes, you can, but again, that is deprecated ...
written 8 days ago by
JC ♦ 10k
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... Cuffdiff is no longer recommended, update your analysis to [HISAT / StringTie / Ballgown][1]
[1]: https://www.nature.com/articles/nprot.2016.095 ...
written 9 days ago by
JC ♦ 10k
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... The method or command could be in the header, but only if that was added. ...
written 10 days ago by
JC ♦ 10k
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Comment:
C: Strand Specificity of Mutations
... Yes, they used methods that can sequence only a specific region relative to the replication origin ...
written 10 days ago by
JC ♦ 10k
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Comment:
C: Public Data Set Download
... Real patient data is no so easy to get, check [EGA][1] and [dbGaP][2] for projects which you can apply for access.
[1]: https://ega-archive.org/
[2]: https://www.ncbi.nlm.nih.gov/gap/ ...
written 10 days ago by
JC ♦ 10k
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... I guess you are trying to install the [VG][1] program, for that I recommend to use [bioconda][2].
[1]: https://github.com/vgteam/vg
[2]: https://anaconda.org/bioconda/vg ...
written 10 days ago by
JC ♦ 10k
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... To load your data you just need to save it in CSV, TSV or similar format, R includes multiple ways to load data from files ([read.table][1]):
data_tsv <- read.table("path/to/file.tsv", header=TRUE, row.names=1)
The next step is just to use the [heatmap.2][2] function to create your image.
...
written 10 days ago by
JC ♦ 10k
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Comment:
C: Strand Specificity of Mutations
... During DNA duplication, you have 2 ways of copy the strands (in [figure 1a][1] in the paper), which causes the duplication process is not the same for the leading and lagging strands. So, you can have new mutations in one copy which are not in the other copy.
[1]: https://genomebiology.biomedcen ...
written 10 days ago by
JC ♦ 10k
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