The Illumina sequencing reads for sample "DL_pool" from run 120406_SN397A_0236_D0KL4ACXX, lane(s) 7 are ready.

Please note that the files are in a *new format* generated by the new Illumina pipeline software (v1.8):

• The sequences are in fastq format. All sequences (raw and pass filter reads) are in a single file, with the pass filter status indicated by a flag (Y/N) in the sequence header for each read."Y" in the header means the read is filtered (out), i.e. flagged as low quality.
• Quality scores are now in Sanger FASTQ format. The offset is ascii 33, instead of the previous Illumina Q score offset (ascii 64).

The read file(s) can be downloaded using one of the following ways:

• Using your web browser, by clicking on the following link(s):

File: 3287_5979_3287_N_DL_pool_R1.fastq.gz:
http://cbsuapps.tc.cornell.edu/Sequencing/showseqfile.aspx?mode=http&cntrl=593850856&refid=3884

• If you intend to download the file(s) to a Linux machine, you may find it more convenient to use the following command(s):

*wget -q -O 3287_5979_3287_N_DL_pool_R1.fastq.gz *
"http://cbsuapps.tc.cornell.edu/Sequencing/showseqfile.aspx?mode=http&cntrl=593850856&refid=3884"

You can run the command(s) above one-by-one in a Linux terminal window, or paste them into a file (making sure there are no blank spaces after the "\" character) and execute that file as a shell script.

• By logging in to the BioHPC web Data Manager site http://cbsuapps.tc.cornell.edu/Sequencing/seqmain.aspx and using the File Manager tool. If you have an account on the CBSU/3CPG Lab Linux workstations, you can log in to BioHPC web using the Lab credentials. Otherwise, please contact CBSU at http://cbsuapps.tc.cornell.edu/contactus.aspx to set up an account.