GSE27218 Processing Pipeline

Publication

Nature neuroscience (2011) — PMID 21358643

Dataset

Disrupted processing of long pre-mRNAs and widespread RNA missplicing are components of neuronal vulnerability from loss of nuclear TDP-43 (RNA-seq)

1. 1

   Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata

   Bowtie v0.12.2 GitHub

   $ Bash example

   # Install Bowtie v0.12.2 if not already installed
   # conda install -c bioconda bowtie=0.12.2
   
   # Ensure the mm8 index is available. This typically involves downloading pre-built indices
   # or building them from the mm8 reference genome FASTA using 'bowtie-build mm8.fa mm8_index'.
   # Replace 'mm8_index' with the actual path to your Bowtie index for mm8.
   # Replace 'reads.fastq' with the path to your pre-processed (trimmed and masked) sequenced reads.
   # The output 'alignment.sam' will contain the alignments.
   bowtie -q -p 4 -e 100 -y -a -m 10 --best --strata mm8_index reads.fastq > alignment.sam

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