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Old 08-04-2010, 12:50 PM   #1
Junior Member
Location: Minnesota

Join Date: May 2008
Posts: 3
Default HiSeq 2000 File Sizes

I was wondering if anyone that is working with a HiSeq 2000 could provide some general file size estimates. I am looking for total file sizes
- per lane, per flow-cell, or per run
- intensity files, .bcl files, FASTq files, and/or BAM files
- for 50, 75, and 100 bp PE and SE runs.

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Old 08-04-2010, 03:30 PM   #2
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Location: USA

Join Date: Apr 2009
Posts: 482

Attached is the site prep guide. It doesn't give the file sizes you want but does recommend computing specs and archiving space.

Have you gotten your HiSeq? I have heard that it can take 6 months or more. Our official ship date is over 3 months from placing the order.
Attached Files
File Type: pdf HiSeq_SitePrep_15006407_D.pdf (110.0 KB, 460 views)
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Old 09-24-2010, 10:42 AM   #3
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Location: Kansas City

Join Date: Mar 2008
Posts: 197

I have a booklet from a user group meeting that lists:

Hiseq 200G run
Image Data 32TB (not tfrd)
Intensity data 2TB (optionally tfrd)
BaseCall / Quality score data .25 TB
Final Alignment output 1.2 TB

GAIIx 50G run
Image Data 5.6TB (optionally tfrd)
Intensity data .5 TB (optionally tfrd)
BaseCall / Quality score data .06 TB
Final Alignment output .3 TB
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Old 09-28-2010, 12:16 PM   #4
Location: Ann Arbor

Join Date: Dec 2008
Posts: 28

Our first HiSeq is being validated now

For 1 36X36 flowcell:

48G per lane .cif data (Intensities/L00X folders)
3.3G per lane of _pos.txt files
200M per lane of .filter files
6.1G per lane of .bcl data (BaseCalls/L00x folders)
40G per lane of _qseq.txt files

Size of BaseCalls folder after BclConverter: 193G
Total size (Intensities/BaseCalls) 728G

You don't have to keep the .cif and the .bcl files, but I wanted to test if running Bustard from .cif gave the same results as Bclconverter -- it did almost exactly.
Christine Brennan
UM DNA Sequencing Core
Ann Arbor, MI 48109
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