User: jmfu

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jmfu10
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Joined:
3 years ago
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Posts by jmfu

<prev • 5 results • page 1 of 1 • next >
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Comment: C: What assays are distributed with Recount TX data
... Hi there, "ses" is the standard errors of the fragments estimates, "scores" is score between 0 and 1 that dictates how uniquely identifiable each transcript is under the model we fit (0 being perfectly redundant, and 1 being perfectly unique). "df" is the degrees of freedom that particular transcrip ...
written 11 days ago by jmfu10
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Answer: A: Using Polyester to simulate large number of reads from a large transcriptome
... What is your sessionInfo() when using the newer version of polyester? ...
written 2.5 years ago by jmfu10
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Comment: C: Using Polyester to simulate large number of reads from a large transcriptome
... 100 mb transcriptome should be easily loaded into memory in one go. If you break it up into 100 pieces should be fine. As for practicality, it is all a matter of perspective. You can just leave the loop to run, and add in a line to let you know how far along the simulation you are. Insert after the ...
written 2.5 years ago by jmfu10
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Answer: A: Using Polyester to simulate large number of reads from a large transcriptome
... Now for the split generation of reads (assume the transcriptome is not too big and can be loaded into memory in one go): fasta = readDNAStringSet(yourfile) transcript_count = length(fasta) # Choose number you want to break simulation up into chunks = 100 # Assign each transcript to a chunk for pro ...
written 2.5 years ago by jmfu10
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Answer: A: Using Polyester to simulate large number of reads from a large transcriptome
... Before I answer how to split the transcriptome and generate reads separately for each piece, I'm going to clear something up for you regarding fold change and the replicates.  When you say you want a fold change of 1.2 for a transcript, this means that for a transcript one sample compared to anothe ...
written 2.5 years ago by jmfu10

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