title: RNA-seq of human brain tissue sample: Sample Pt-0227-DIPG-RNA-Normal
design: "RNA-seq libraries were constructed using the standard TruSeq poly(A)+ RNA protocol (Illumina). Sequencing was performed on either a HiSeq 2000 (Illumina) or HiSeq 2500 (Illumina). Sequence assembly was performed using either CASAVA (Illumina) or Bcl2Fastq (Illumina). All transcriptome libraries were sequenced with the Illumina HiSeq in paired end mode. The reads that passed the chastity filter of Illumina BaseCall software were used for subsequent analysis. We trimmed all reads to 85-mers and aligned them to the reference human genome (NCBI build 36.1, hg18) using Bowtie in single read mode, keeping unique best hits and allowing up to two mismatched bases. Next, all of the exons for a single gene were concatenated to form a single 'transcript' for that gene.  Reads that mapped to the exons in the gene, as well as reads that mapped to the splice junctions, were remapped to the transcript.  We then walked the transcript and summed the coverage at each position, then divided the result by the transcript length x the number of reads in the sample, and then multiplied the result by one million. This method is a modified version of the one described in ""Mapping and quantifying mammalian transcriptomes by RNA-Seq"" (Nature Methods)."
attributes.tag: alignment_software
attributes.value: Bowtie