cellranger count preserve the STAR alignment log output (Log.out) files?
Answer: The STAR output logs are not preserved by
The Cell Ranger pipeline splits the initial input FASTQ files into chunks. STAR runs on each chunk separately and generates a log file for each chunk. The intermediate outputs from these chunks, including the STAR logs, are removed by the pipeline to save disk space.
Summary information such as the genomic distribution of mapped reads (intergenic, intronic, exonic, antisense) is provided in the web summary file.
Alternatively, the Cell Ranger BAM output file can be queried directly or summarized based on the FLAG, MAPQ, and a variety of other features described on our support site here.