These dataset were generated from the publicly available raw FASTQ files of the Mouse Olfatory Bulb Replicates number 4 and 9 from the publication http://science.sciencemag.org/content/353/6294/78
The data was analysed with the ST Pipeline 1.3.1 and with a STAR genome index generated from the Mus Musculus Ensembl annotation version 86. The annotation file used Mus Musculus GenCode 25 vM11. A contaminant genome STAR index was used generated from the Ensembl non conding RNA Mus musculus version 86. The IDs file used to demultiplex were the 1000L2 and 1000L5.
The following settings were used:
st_pipeline_run.py
--output-folder OUTPUT
--ids id.txt
--ref-map path_to_genome_index
--ref-annotation path_to_annotation_file.gtf
--expName SOME_NAME
--remove-polyA 10
--remove-polyT 10
--remove-polyG 10
--remove-polyC 10
--htseq-no-ambiguous
--verbose
--mapping-threads 16
--log-file OUTPUT_log.txt
--two-pass-mode
--umi-filter
--filter-AT-content 90
--filter-GC-content 90
--contaminant-index path_to_contaminant_index
--min-length-qual-trimming 30
--disable-clipping
R1.fastq R2.fastq