User: story.benjamin

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Posts by story.benjamin

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Comment: C: Pulling Genbank Annotation Information via library(genbankr)
... So I think the problem has something to do with the command: exns = stack(exns) which is made by the make_exongr() function, made by make_gbrecord(), which is made by the original readGenBank() command I hacked together a workaround for my purposes but I'm not sure if this is a bug or a 1-off sc ...
written 5 weeks ago by story.benjamin0
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Pulling Genbank Annotation Information via library(genbankr)
... I am trying to pull a specific GenBank entry off of the NCBI database using the genbankr library. My hope was to have all the feature information in a more "R friendly" (e.g. GRanges) format so I could incorporate it into my analysis. Other IDs seem to work but this one was giving me trouble. This ...
annotation genbankr genbank written 5 weeks ago by story.benjamin0
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rtracklayer - export.bw bug
... Hi, A colleague approached me in hopes of figuring out a strange export problem they were having with rtracklayer. For some reason it seems that when I have over 255-256 chromosomes (manual tested this) in a genome, that certain chromosome(s) are lost during the export of a bigwig. This was notice ...
rtracklayer bigwig export.bw written 23 months ago by story.benjamin0 • updated 23 months ago by Michael Lawrence10k
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Comment: C: Empty SQL query result for SRA run
... I am also getting this error for specific datasets. It seems somewhat random. SRP051830 is an example of one that doesn't work.   EDIT: What did work is to set the fileType = 'sra'  ... so perhaps it's an issue with fastq availability. Downside is obviously that you have to do the sra --> fastq ...
written 23 months ago by story.benjamin0

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