Editing BioMicroCenter:FAQ (section)

== DOWNLOADING DATA ==
You will be notified by email that your data is ready. The data will be placed on one of our servers for you the download. All data is typically retained for 60 days. We STRONGLY encourage you to keep a local copy of your data as soon as possible. Contact [mailto:bmc-data@mit.edu bmc-data@mit.edu] if you have any issues.

=== MIT / MIT-CERTIFICATE + VPN ===
{| class='wikitable'
 |'''LURIA'''||
* samples can be directly copied from our share /net/bmc-pub17/data/bmc/public/[LAB]/[PROJECT]
* Please ensure you are running cp from a COMPUTING NODE of Luria instead of the head node
 |-
 |'''Windows/Mac SFTP client||
* Mac: Fetch | Windows: SecureCRT/FX. Download from [https://ist.mit.edu/software/filetransfer Secure File Transfer at MIT]
 |-
 |'''Web Download <p> (MIT certificate required)'''||
https://bmc-data.mit.edu/[LAB]/[PROJECT]
|}

=== NON-MIT ===
Non-MIT users should use a SFTP client to connect to bmc-150.mit.edu with credentials emailed to you. SSH or SCP is not supported.
{| class='wikitable'
  |'''WINDOWS/MAC'''||
* SFTP client recommended: [https://filezilla-project.org Filezilla]
* A screenshot of FileZilla [[Image:FileZillaScreenshot.jpg|500px]]
  |-
  |'''UNIX / LINUX'''||
* Samples can be copied from our servers using ''sftp'' and the credentials provided.
|}
Please contact [mailto:bmc-data@mit.edu bmc-data@mit.edu] if you have difficulty obtaining your data.

=== Read archival ===

Users are strongly encouraged to retain a local copy of their data as early as possible after sequencing result delivery. 

<b>After 60 days, fastq files will be compressed on the server. Bam files, containing reads aligned either to the genome mentioned in the sample submission form or phiX (a phage genome), will be deleted to save storage space.</b><BR><BR>

Older files: Prior to 2020, bam files were maintained as archival files. Fastq files can be regenerated from the bam files (samtools sort -n to sort bam files by read names, and converted back to fastq files using bedtools bamToFastq).