User: andrewelamb

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Posts by andrewelamb

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error with base-level DERfinder using large sample sizes
... I've gotten base-level DERfinder to work with smaller groups ~12 BAM files, but when i try on our larger experiment ~500 BAM files I'm running into an issue:2 2017-03-15 10:12:00 fullCoverage: processing chromosome 9 2017-03-15 10:12:03 loadCoverage: finding chromosome lengths 2017-03-15 10:12:03 l ...
derfinder written 2.4 years ago by andrewelamb0 • updated 2.4 years ago by Leonardo Collado Torres650
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Comment: C: Issue creating a genomic state object in derfinder from an Ensembl GTF file
... Thanks! I'll see if the Bumphunter documentation has anything to say. ...
written 2.5 years ago by andrewelamb0
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Comment: C: Issue creating a genomic state object in derfinder from an Ensembl GTF file
... Hi Leo, everything above worked, but I'm having another issue now. Using the script that wa sworking before but with the new GRCH38 txdb, the out put of matchGenes isn't quite right. The, columns, name, annotation and geneL, are all NA's.  Any Idea what this might be?   annotation_obj <- annota ...
written 2.5 years ago by andrewelamb0
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Comment: C: Issue creating a genomic state object in derfinder from an Ensembl GTF file
... Oh I see, somehow I missed that line. Thanks! ...
written 2.5 years ago by andrewelamb0
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Comment: C: Issue creating a genomic state object in derfinder from an Ensembl GTF file
... Thanks for all your help Leo. library(GenomicFeatures) library(derfinder) library(devtools) library(rtracklayer) gr <- import('ftp://ftp.ensembl.org/pub/release-81/gtf/homo_sapiens/Homo_sapiens.GRCh38.81.gtf.gz') gr_small <- keepSeqlevels(gr, c('Y', 'MT'), pruning.mode = 'tidy') Error in ke ...
written 2.5 years ago by andrewelamb0

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