User: danielle.bilodeau

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Posts by danielle.bilodeau

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Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Hi Julie, Thanks for your patience while I made the change you recommended. I now have a new fasta file with only the chromosome name in each header. Here's an excerpt: ``` $ grep ">" glamblia34.fa >GLCHR01 >GLCHR02 >GLCHR03 >GLCHR04 >GLCHR05 >AACB02000013 >AACB02000029 `` ...
written 6 months ago by danielle.bilodeau0
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Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Thanks for the grep tip! Here's what I get when I look for ">" in my fasta file (I removed the middle lines to make it shorter): ``` $ grep ">" gl34.fa >GLCHR01 | organism=Giardia_Assemblage_A_isolate_WB | version=2013-02-08 | length=1491578 | SO=chromosome >GLCHR02 | organism=Giardia_ ...
written 6 months ago by danielle.bilodeau0
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Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Hi Julie, It definitely makes sense, but I'm not sure why the BSgenome wouldn't have those chromosome names. The seqnames in the GRange object were taken directly from the same genome I used to forge the BSgenome. I suppose my question then is, where does the BSgenome obtain the chromosome names f ...
written 6 months ago by danielle.bilodeau0
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Comment: C: Unable to generate feature vector with custom genome in cleanUpdTSeq
... Hi Julie, Here's the output: ``` > peaks_grange GRanges object with 3850 ranges and 1 metadata column: seqnames ranges strand | score | GL50803_10013_42 GLCHR03 1211025 + | 1 GL50803_10014_486 GLCHR03 1212644 ...
written 6 months ago by danielle.bilodeau0
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Unable to generate feature vector with custom genome in cleanUpdTSeq
... Hello, I am using the cleanUpdTSeq package to analyze a set of potential 3' UTRs in the parasite Giardia lamblia. I am working from a dataframe with the coordinates of putative 3' UTRs, as per the package requirements. The issue arises with the function "buildFeatureVector" which adds the upstream ...
bsgenome cleanupdtseq bsgenomeforge written 6 months ago by danielle.bilodeau0 • updated 6 months ago by Julie Zhu4.0k

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