MBGProject: Online extract SAGE library sequences and tag counts from sequences.

Extract SAGE library sequences and tag counts from sequences or chromatographs

Submit a ZIP file containing all library sequence runs: extract the sequences and quality values using PHRED or the ABI base caller and compress the files in a single ZIP archive. Each sequence run needs to have a file with the extension ".phd.1" (PHD file) or a pair of files with the respective extensions ".seq" and ".qual" (FASTA like format).
(For internal users only it is also possible to submit the chromatograph files and PHRED will be run on the server - these files may however be very large and this might take a while.)

E-Mail Address:

ZIP archive containing all sequence runs:
(Download example input chromatograph files or input phd files)

Upload file:

Library name (to appear in the results file):

File type: chromatographs (only internal users), base caller output, phd files or seq/qual pairs.

Taglength to extract: 10 bases, 17 bases.

Ditaglength, Minimum: 20 bases, 32 bases; Maximum: 24 bases. 36 bases.

Remove duplicate ditags: yes, no.

Remove all tags that contain N: yes, no.

Remove tags that are potential artifacts: SAGE linkers, ribosomal RNAs, mitochondrial.

Remove tags where average quality score is less than

Default quality value (used for all bases if quality files are missing).

Cut site

Output format: complete library including all tag sequences and counts, only tag counts.

Last modified: 07.06.2004

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