Occasionally, large files become corrupted during download. You can determine whether this has occurred by comparing the checksum of a file before and after download. We have placed checksums for your fastq.gz files in your run directory in a file called md5sum.txt. Compare the values in this file to new checksums calculated on your downloaded files.

To calculate a checksum for a file called myfile.fastq.gz, use the GNU md5sum utility:

md5sum myfile.fastq.gz

If the checksums for a file before and after download differ, then the file is corrupt or incomplete and should be downloaded again.

To calculate and compare the checksums of all FASTQ files listed in md5sum.txt:

md5sum -c md5sum.txt