Chunk #7 — Materials and Methods — RNA-seq

Source

Alcohol Causes Lasting Differential Transcription in Mushroom Body Neurons.

Embedded

yes

Text

1.0.136 (Wickham 2009). No samples were discarded and default settings were used for the pipeline unless otherwise noted; command line code as follows:#Trimmomatic:TruSeq3-SE.fa:2:30:10:8:true LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36#HISAT2:hisat2 -q -x <reference index> -U <input fastq file> -S <output sam file> -p 50#Samtools:samtools view -Su alns.sam | samtools sort -o alns.sorted -@ 4#StringTie:stringtie <input.sorted.bam> -b <path to Ballgown tables> -o <output.gtf> -G <reference.gtf>