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Problem in running Glimmer3

Hello everyone i am beginner user in linux. I have installed glimmer3 in linux. The problem is that i dont know where to input my sequence and how to build ICM in glimmer. I have also read glimmer tutorial I cannot understand it.

glimmer
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updated by h.mon h.mon • written by talhar123456 • talhar123456

1 answer

i dont know where to input my sequence

USAGE:  glimmer3 [options] **<sequence-file>** <icm-file> <tag>

i dont know how to build ICM

The only input needed is your genome:

long-orfs -n -t 1.15 **genome.fasta** run1.longorfs
extract -t genome.fasta run1.longorfs > run1.train
build-icm -r run1.icm < run1.train

Page 4 of Glimmer3 manual mentions the g3-from-scratch.csh script that runs the whole pipeline:

g3-from-scratch.csh genome.fasta

If these instructions are too complicated, you have to be more specific about what you tryed and the error messages thrown.

• 1 views • link
written by h.mon h.mon

Thank you for responding to my query but I am still facing following problem hope you will help me out

glimmer3 [options] <sequence-file> <icm-file> <tag> Can you please elaborate what should i write in the [options], <sequence-file>

Also tell me the exact command which i should copy paste

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written by talhar123456 • talhar123456

What is the name of the file with your genome? (this is more a hint than a question)

edit: I already gave you a copy-pasteable command:

g3-from-scratch.csh genome.fasta
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written by h.mon h.mon

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