User: joe

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joe60
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Posts by joe

<prev • 30 results • page 1 of 3 • next >
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Comment: C: From ensembl id to protein structure
... Ah, right. Good catch! ...
written 11 hours ago by joe60
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Comment: C: Generating consensus sequence from bam file
... 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 joe60
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Comment: A: gene name to protein structure download
... 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 joe60
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Comment: C: From ensembl id to protein structure
... 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 joe60
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Answer: A: From ensembl id to protein structure
... 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 joe60
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Answer: A: Local protein BLAST not working
... 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 joe60
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Comment: C: How extract data from gnomAD for some genes?
... 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 joe60
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Answer: A: How extract data from gnomAD for some genes?
... 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 joe60
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CRISPR off-target validation with GUIDEseq
... 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 ...
crispr circleseq cas9 guideseq written 13 days ago by joe60
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Comment: C: bwa mem -R (RGline) format for DNBseq fastq
... 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 ...
written 24 days ago by joe60 • updated 24 days ago by genomax71k

Latest awards to joe

Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: mclapply on AWS
Scholar 6 weeks ago, created an answer that has been accepted. For A: mclapply on AWS

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