GSE27201 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 (CLIP)

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 (if not already installed)
   # conda install -c bioconda bowtie=0.12.2
   
   # Note: The description mentions trimming and masking steps prior to alignment.
   # These steps are not included in this Bowtie command but would typically precede it.
   # Example placeholders for input reads and reference index:
   # reads.fastq: Your input FASTQ file containing sequenced reads.
   # mm8_index: The path to the Bowtie index for the mm8 whole genome.
   #            (e.g., /path/to/mm8_index/mm8)
   
   bowtie -q -p 4 -e 100 -y -a -m 10 --best --strata mm8_index -U reads.fastq > aligned.sam

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