Author: Timothy A. Dinh; Ramja Sritharan; F. Donelson Smith; Adam B. Francisco; Rosanna K. Ma; Rodica P. Bunaciu; Matt Kanke; Charles G. Danko; Andrew P. Massa; John D. Scott; Praveen Sethupathy
Title: Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance Document date: 2020_1_18
ID: bf4qpsy7_74
Snippet: Read quality was assessed using FastQC. Reads were trimmed, mapped, and quantified to the hg19 genome using miRquant 2.0, our previously described smRNA-seq analysis pipeline (Kanke et al., 2016) . Briefly, reads were trimmed using Cutadapt and reads were mapped to the genome using Bowtie (Langmead et al., 2009) . Perfectly aligned reads represented miRNA loci and imperfectly mapped reads (from isomiRs) were re-aligned to these loci using SHRiMP .....
Document: Read quality was assessed using FastQC. Reads were trimmed, mapped, and quantified to the hg19 genome using miRquant 2.0, our previously described smRNA-seq analysis pipeline (Kanke et al., 2016) . Briefly, reads were trimmed using Cutadapt and reads were mapped to the genome using Bowtie (Langmead et al., 2009) . Perfectly aligned reads represented miRNA loci and imperfectly mapped reads (from isomiRs) were re-aligned to these loci using SHRiMP (Rumble et al., 2009 ). Aligned reads were quantified and normalized using reads per million mapped to miRNAs (RPMMM).
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