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Instructions to Download and Process BAM files of 1.3 Million Brain Cells

BAM files have been deposited with GEO (id: GSE93421) and can be downloaded from SRA (id: SRP096558). They can be downloaded free of charge.

1. Download the files

We recommend downloading the original bam files that were deposited at SRA here, as some of the 10x custom tags are not kept in files processed and converted by the SRA toolkit. The 'prefetch' function is not recommended. Note, it took us ~48 hours to download all the BAM files with aria2c, and the download time may be higher or lower depending on your connection. In our experience, aria2c is a ~4x times faster than wget.

  • An example of wget command: wget http://sra-download.ncbi.nlm.nih.gov/srapub_files/SRR5167880_E18_20160930_Neurons_Sample_01.bam
  • An example of aria2c command: aria2c http://sra-download.ncbi.nlm.nih.gov/srapub_files/SRR5167880_E18_20160930_Neurons_Sample_01.bam
  • An example of a shell script to download all the files using aria2c using the maximum allowable number of connections: aria2c -x16 -i url_list
    • To put the script in the the background, add & disown to the end of the command.
    • To adjust the number of parallel downloads, use the -j function.

2. Convert 10x BAM files to FASTQs

Please follow the instructions here to convert 10x BAM files to FASTQ files.

Document Type
Technical Note

Last Modified
June 14, 2022