GSE64078 Processing Pipeline
OTHER
code_examples
1 step
Publication
ALS-causative mutations in FUS/TLS confer gain and loss of function by altered association with SMN and U1-snRNP.Nature communications (2015) — PMID 25625564
Dataset
GSE64078ALS-causative mutations in FUS/TLS confer gain- and loss-of-function by altered association with SMN and U1-snRNP
Warning: Pipeline descriptions and code snippets may be inferred or AI-generated. Use them only as a starting point to guide analysis, and validate before use.
Processing Steps
Generate Jupyter Notebook-
1
The sequenced 40 bases were mapped to the oligo pool sequences with Bowtie by allowing 1 mismatch in each of the donor and acceptor sequences.
$ Bash example
# conda install -c bioconda bowtie=1.2.2 # Assume 'oligo_pool.fasta' contains the oligo pool sequences. # Assume 'reads.fastq' contains the sequenced 40 bases. # Build Bowtie index for the oligo pool sequences # bowtie-build oligo_pool.fasta oligo_pool_index # Map the 40-base reads to the oligo pool sequences # -v 1: Allow up to 1 mismatch in the alignment # -l 40: Set the seed length to 40 (the full read length) # -a: Report all valid alignments for each read # -S: Output alignments in SAM format bowtie -v 1 -l 40 -a -S oligo_pool_index reads.fastq output.sam
Raw Source Text
The sequenced 40 bases were mapped to the oligo pool sequences with Bowtie by allowing 1 mismatch in each of the donor and acceptor sequences. Genome_build: hg18 Supplementary_files_format_and_content: The processed files contain both the genomic location (the first 6 columns) and counts for 2 isoforms (last 2 columns) of each alternative splicing event.