Moderator: dariober
dariober ♦ 9.0k
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Posts by dariober
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Answer:
A: GATK gradlew bundle Error
... I surmise this has nothing to do with GATK but with gradle. Googling `java.security.ProviderException: java.security.InvalidKeyException: EC parameters` leads to this [issue][1] which suggests OpenJDK7 is the culprit. As suggested there, try upgrading to OpenJDK8 in case you are also on 7. This is, ...
written 23 hours ago by
dariober ♦ 9.0k
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... Is it still the case that picard (MarkDuplicates?) chokes on split reads? I would check that first. Using `-M` option is a hack to make picard work but it would be better avoiding it since the shorter split of a read is not a "secondary alignment" and there is nothing necessarily wrong with split re ...
written 12 days ago by
dariober ♦ 9.0k
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... Out of curiosity, where did you get `readCounter` from? At a glance I don't see it in [HMMcopy][1].
Does your downsampled bam have any reads at all? Try `samtools view -c input_15X.bam` or just `ls -lh input_15X.bam` to see if it has a decent size.
[1]: https://bioconductor.org/packages/rel ...
written 13 days ago by
dariober ♦ 9.0k
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... Just to demystify the "genome file"... This is just a tab-separated table with one row per chromosome giving chromosome name and size like `chr1 247249719` (I don't remember if the file name has to end with `.chrom.sizes`). So it is quite simple and you could prepare it by yourself.
For hg18 I thi ...
written 13 days ago by
dariober ♦ 9.0k
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... Hi- some random thoughts...
> the overlap goes to at least 80%
I think that depends a lot on the particular sample(s) you are looking at. If you have variants with high frequency than both methods should pick them up. As you go towards lower allele frequencies then the discrepancy inevitably in ...
written 17 days ago by
dariober ♦ 9.0k
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... If you are looking for an exploratory analysis directly from the command line you could try [ASCIIGenome][1] (I'm the author). Something like:
ASCIIGenome gene.bed chipseq1.bed chipseq2.bed ...
Would give you something like [this][2] ![enter image description here][3]
[1]: http://asciigenome. ...
written 27 days ago by
dariober ♦ 9.0k
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... Hopefully you get the idea. But on reading again your question make sure that what you need is instead the H matrix of the transpose of the expression matrix. ...
written 28 days ago by
dariober ♦ 9.0k
3
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... I think what you want is the W matrix which you can get with the `basis` command (NMF package), E.g.:
# A matrix of 20 genes and 10 samples
mat<- matrix(runif(n= 200, min= 0, max= 100), nrow= 20, ncol= 10)
library(NMF)
res<- nmf(mat, rank= 2)
w<- basis(res)
h&l ...
written 29 days ago by
dariober ♦ 9.0k
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... Some wild guess...
> bigwig file it seems to I have lots of read in rRNA locus
This may be due to some rescaling when converting bam to bigwig. For example, rescaling to have library size 10M reads will appear as having more reads compared to rescaling to have 1M reads. (Such rescaling can be ...
written 29 days ago by
dariober ♦ 9.0k
1
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... Among the many programs that I hacked together, there is [MarkovSequenceGenerator][1] which may be you can make use of. As I remember, just like the OP, I needed a null distribution of sequences matching nucleotides and di-nucleotide content. So this program shuffles sequences in a fasta file using ...
written 4 weeks ago by
dariober ♦ 9.0k
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