FAQ
Q. What information and data will I receive after my sample has been sequenced?
A. You will receive all reads in the FastQ format, demultiplexed via openBIS. Data generated for groups at the Biozentrum and FMI are also directly transferred via the BC2 network. We also perform external pageFastQCcall_made analysis of all datasets. QC data is available via openBIS.
Q. What is the size of a FastQ file?
A. This depends on the type of sequencing run and the amount of reads generated. Average gzipped FastQ size per HiSeq 2500 lane: SR50, 8-10 Gigabyte (GB); PE125, 20-25 GB. We usually distribute the reads in FastQ packages of 50mio reads. Gzipped 50mio FastQs of 50/125 base reads have 2.5/5 GB, after unzipping 7.5/15 GB.
Q. What are FastQ files carrying no index but 'undetermined' in their file name?
A. When sequencing a pool of indexed libraries ('multiplexing') compliant to the Illumina protocol (separate index read; no in-line or initial barcode) the reads are demultiplexed according to their index read. For each index a separate FASTQ file is generated. If index reads cannot be assigned to one of the given indexes, e.g. they contain sequencing errors, the demultiplexing software writes those reads in an extra file called 'undetermined'. An optimal demultiplexing process leads to <5% undetermined reads.
Q. How many errors do you allow in the index/barcode read?
A. By default we don't allow mismatches in the sequenced index read.
Q. How many reads can I expect from my run?
A. Runs can vary from sample to sample, depending on the quality of the starting material and type of library. We typically see 200-250 million clusters passing filter per HiSeq 2500 lane and 300-450 mio NextSeq 500 high output run.
Q. What if my run fails due to hardware or reagents, am I charged twice?
A. All quality metrics for each run are closely monitored. Any failure due to hardware or poor reagents will be rerun at no additional charge after repairs or replacements are made. Every attempt will be made to quickly restart a failed run.