Genome alignments for the project "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol" - Protocol optimization

Genome alignments for data generated in the project "Whole transcriptome analysis of thousands of FACS-sorted single cells with the single cell nanoCAGE protocol – Optimization of the protocol." Files names indicate unique identifiers of MOIRAI workflow runs, with the following structure: library name, dot, workflow ID (OP-WORKFLOW-CAGEscan-short-reads-v2.0.), dot, timestamp. The raw (FASTQ) data of each library is also deposited in Zenodo (10.5281/zenodo.250156). Library names correspond to the following runs:

•  NC33: 151007_M00528_0161_000000000-AEBDC
•  NC37: 151204_M00528_0173_000000000-AEBEF
•  NC38: 151211_M00528_0175_000000000-AE9PJ
•  NC39: 160122_M00528_0185_000000000-AEB18
•  NC42: 160302_M00528_0192_000000000-AELYK

This data can be analysed using the "CAGEr" software package available from Bioconductor.  The "multiplex_files.zip" file contains tables indicating which samples are biological replicates of each other or negative controls.