Viewing and Retrieving Data

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Viewing and Retrieving Data Here is some basic
information for using the new DAF ordering and
data server. For more detailed information please
see the Advanced PowerPoint presentations.
If you have further questions, please contact
Breon or Caron at (4-6548), Roxann (410)
859-3085, or Duane (4-0196).
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Email Notification
Requests become complete when all samples attain
the status of Complete, C or Failed, F.
An email notification is sent automatically by
the server. Therefore, it is important that DAF
has a valid email address for EACH user
/Finch/SRM/requestDetails?REQ_ID387
Click link or cut paste into your
web browser. Please add http//finch.daf.jhmi.edu
to beginning of address given
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Viewing the Request
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Viewing the Data
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Understanding Phred Values
Quality -10 log10 (probability of error)
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Understanding Trim Length
Low quality bases in the middle of a sequence are
NOT trimmed.
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Understanding Is Vector
http//www.ncbi.nlm.nih.gov/VecScreen/UniVec.html
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Understanding Short Insert
The Finch-Server identifies vector sequence on
both ends of the read using the cross_match
algorithm against the UniVec database. In a
genomic project, it is wasteful to sequence known
vector sequences.
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Understanding Screen Positives
The Finch-Server identifies E. coli genomic
sequences using cross_match. Useful in
identifying host DNA contamination.
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Viewing single chromat details
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Viewing single chromat details
Phred Quality by Base Position
FASTA Sequence. Can cut and paste.
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Viewing single traces
Note Low quality region indicated on Trace and
Phred Quality Graph
Now that all data is viewable via a web browser,
we will no longer print chromats
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Viewing the Folder Report
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Folder Report Details
Use links to find subsets of reads
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Downloading Files (1)
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Downloading Files (2)
The default values tend to be the most convenient.
Multi-sequence FASTA file all files
concatenated into 1 file. Tar File of FASTA
files all files compressed and downloaded as 1
file, but uncompress into n files.
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Downloading FASTA Files
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Downloading Quality Score Files
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Downloading Electropherograms
On a PC, you may need to use a combination of
WinZip and Aladdin Expander, instead of StuffIt
Expander.
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Downloading Phred Files
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Downloading multiple files
You can download FASTA text, phd, and
chromatogram files.
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Additional Chromatogram Viewers