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Examples

Screen the readings whose names are stored in fofn against a batch of possible contaminant sequences whose names are stored in vnames. Write the names of the readings that pass to file p and those that fail to file f. Increase the maximum sequence length to 5000,000 characters and require a minimum match of 20.

screen_seq -i fofn -s vnames -p p -f f -l20 -m5000000 

Screen the single reading stored in xpg33.g1 against a batch of possible contaminant sequences whose names are stored in vnames. If the reading does not match write its name to file p, otherwise to file f. Increase the maximum sequence length to 5000,000 characters and require a minimum match of 20.

screen_seq -I xpg33.g1 -s vnames -p p -f f -l20 -m5000000 

Screen the readings whose names are stored in fofn against a single possible contaminant sequence stored in ecoli.seq. Write the names of the readings that pass to file pass and those that fail to file fails. Increase the maximum sequence length to 5000,000 characters and require minimum match of 20.

screen_seq -i fofn -S ecoli.seq -p pass -f fails -l20 -m5000000 

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This page is maintained by James Bonfield. Last generated on 2 Febuary 1999.
URL: http://www.mrc-lmb.cam.ac.uk/pubseq/manual/vector_clip_15.html