User: Song Li

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Song Li60
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8 years, 10 months ago
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8 years, 10 months ago
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s********@gmail.com

Posts by Song Li

<prev • 6 results • page 1 of 1 • next >
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Comment: C: countOverlaps() only count positive strand (from GenomicRanges example)
... Hi Martin and Vincent, Thank you for the replies and both methods work, Cheers, Song On Mon, Dec 13, 2010 at 2:19 PM, Martin Morgan wrote: > On 12/13/2010 10:09 AM, Song Li wrote: >> Hi Martin and Vincent, >> >> Thank you for your replies, here is my code: >> >>& ...
written 8.9 years ago by Song Li60
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Comment: C: countOverlaps() only count positive strand (from GenomicRanges example)
... Hi Martin and Vincent, Thank you for your replies, here is my code: > strand(exonRanges)<-"*" Error in `strand<-`(`*tmp*`, value = "*") : replacement 'value' is not an AtomicList with the same elementLengths as 'x' > levels(strand(aligns))<-c('*','*','*') Error in function (class ...
written 8.9 years ago by Song Li60
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countOverlaps() only count positive strand (from GenomicRanges example)
... Hi All, I was following the example in the "GenomicRanges Use Cases", section 3, "Simple RNA-seq Analysis", by "copy-paste" command from the document from page 7 to page 8: What I found out is that countOverlap() only count reads aligned to positive strand. There are 28 reads map to region GRList ...
written 8.9 years ago by Song Li60 • updated 8.9 years ago by Jason Lu190
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Comment: C: Question about TranscriptDb and makeTranscriptDb method
... Hi Herv? , Thank you for the reply. I am little worried about the warning message that "CDS" is not available. However, it does not seem to be a crucial factor to consider at this moment. Best, Song 2010/12/11 Hervé Pagès : > Hi Song, > > On 12/10/2010 11:16 AM, Song Li wrote: >> ...
written 8.9 years ago by Song Li60
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Question about TranscriptDb and makeTranscriptDb method
... Hi, All, I want to thank you for the incredible package which greatly simplifies our analysis for RNA-seq. However, I am working with Arabidopsis RNA-seq data, however, it seems that I have to build a transcriptDb object by myself. Is there a function that reads GTF file and make transcriptDB obj ...
transcriptdb written 8.9 years ago by Song Li60 • updated 8.9 years ago by Hervé Pagès ♦♦ 14k
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ToggleProbe() and Arabidopsis annotation file ath1121501.db.
... Hi All, I was loading Arabidopsis ath1121501.db package using some old code to check my results from several years back. I got the following message: """ Warning: All Arabidopsis packages now require you to use the toggleProbes() method in order to expose multiple mappings. """ I googled and fi ...
ath1121501 probe annotationdbi written 8.9 years ago by Song Li60 • updated 8.8 years ago by Marc Carlson7.2k

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