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The simulation results can be reproduced using the R transcript file available via > file.show system.file("multcomp_VA.R", package = "multcomp")) JS thanks Lea Vaas for drawing his attention to reference [13].
We performed a simple open reading frame analysis (ORF) on all of the Sm454ESTABI transcripts to identify the longest putative protein that could be coded for by each transcript file (Dataset S5).
The AgamP4.1 transcript file was used for identifying piRNAs mapping to genes in An. gambiae.
The transcript file was reduced to contain only transcripts residing entirely within intergenic regions using a previously designed script [ 26].
Reads were aligned to mouse genome (mm9) using TopHat (Trapnell et al, 2009) (version 2.0.9) with default parameters using RefSeq transcript file for coding genes from UCSC.
Pooled non-normalized reads were aligned to the unfiltered Trinity.fasta transcript file using bowtie 0.12.7 [ 31], through the alignReads.pl script distributed with Trinity.
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"We have several investigations ongoing right now, varying from individual homicides, organized crime homicides and organized crime and drug investigations occurring in various locations in Canada today [where] our capabilities in this environment are a significant factor," Flynn said, according to a 2015 transcript filed with the court.
The RA and control transcript files were compared to the reference genome using Cuffcompare to filter out previously discovered transcripts.
Because only psRNATarget and TAPIR accept user-submitted transcript files, only these two predictors are considered here.
Transcript files were imported to an open-source qualitative analysis program, Weft QDA 1.01 (http://www.pressure.to/qda/) for analysis.
Data which are collected in computer file format (ie, data obtained through the Department of Human Services and HNELHD and interview audio and transcript files) will remain in computer file format.
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