User: joe
joe • 60
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Posts by joe
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... Thanks for this! I have a question about tweaking the commands to have the consensus sequence report a "wobble" base in cases of heterozygosity, for example an R would be reported where a SNP is heterozygous for G/A. Do you think this is possible to implement in your pipeline? I'm writing in the con ...
written 11 hours ago by
joe • 60
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... I answered this on your other post...
[https://www.biostars.org/p/398893/#399159][1]
[1]: https://www.biostars.org/p/398893/#399159 ...
written 12 hours ago by
joe • 60
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... The point is that you can use `getBM()` to match the ENSG to the PDB id, and once you have the PDB id you can retrieve the structure info...here I do the first part for you...I recommend the `bio3d` [package][1] for part two
library(biomaRt)
ENSG.list <- c("ENSG00000088305", "ENSG00 ...
written 17 hours ago by
joe • 60
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... The R package `biomaRt` may help you with connecting the ensembl ID to RefSeq or PDB ID. Below is an example linking a gene name to an ensemble ID and Refseq ID, where the `gene.name` is provided by you...but the values input and attributes output can easily be changed according to what you have and ...
written 1 day ago by
joe • 60
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... This sounds more like a file permissions issue. Look up `chmod` and check the permissions granted to your file(s) with regards to read/write/execute...Also, depending on your OS, `stdout` and `stderr` may not do what you want. To be on page with most everyone, I recommend to use a Unix terminal cmd ...
written 1 day ago by
joe • 60
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... Well thank goodness for high standards...below is a bit more which addresses your concerns, although the transcript should be known along with the gene name and the vcf files should be downloaded locally via ftp or gs (or from web browser) [here][1]
This will also require `RMySQL` and I show here ...
written 1 day ago by
joe • 60
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... From R you can use the packages `GenomicRanges` and/or `VariantAnnotation` and/or `vcfR` and follow this workflow;
#defines the region you want to look at
rngs <- GRanges(chr, IRanges(query.start,query.end))
names(rngs) <- gene.name
param <- ScanVcfParam(which=rngs)
th ...
written 1 day ago by
joe • 60
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... I have a top-level question regarding the GUIDEseq analysis pipeline. Why is there a huge discrepancy between the number of on-/off-targets identified and the number of reads in the input data? Based on the principles of the library preparation it seems that many more reads would be usable.
For exa ...
written 13 days ago by
joe • 60
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... I have multiple paired-end samples, which is why I was hoping to use -R. This is the header I was provided from the NGS company (BGI), which used DNBseq machines. The only documentation I could find from them shows the below.
FASTQ file sequenced by DNBseq.
@CL100072652L2C001R001_12/1
GCGA ...
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