How to access your sequencing data

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When sequencing runs are finished, we automatically upload FastQ files to a client’s Box.com account.  These files are typically found in the directory:

ClientName->Reports->ReportID->FastQ

The FastQ files in this directory adhere to the following naming convention:

ClientName_ProjectID_SampleID_SampleName_sometext_R1_sometext.fastq.gz

ClientName_ProjectID_SampleID_SampleName_sometext_R2_sometext.fastq.gz

 

ClientName = the name of the client’s organization

ProjectID = a SeqCenter internal project identifier (you can generally ignore this)

SampleID = a SeqCenter internal sample identifier (you can generally ignore this)

SampleName = this is the sample name supplied to the SeqCenter by the client; it typically corresponds to the sample vial name

sometext = a text string added by the sequencer (you can ignore this)

R1 = the forward read identifier

R2 = the reverse read identifier

fastq = identifies this as a file in FastQ format

gz = the files are compressed in gzip (“.gz”) format

In most, but not all, sequencing runs we use paired-end reads.  There is a forward read and a reverse read, which together form a single paired-end read.  The R1 and R2 monikers refer to these individual reads. The forward reads and reverse reads are stored in separate files.  Many bioinformatics applications expect these two files to be processed together so you can keep track of them with the R1 and R2 identifiers.