[Automated-sequencing] Need help using phred , cross_match and phrap

talanki via autoseq%40net.bio.net (by ltalanki At gmail.com)
Thu Nov 9 14:43:30 EST 2006


Hi,

I am trying to assemble sequences using the phred,cross_match and phrap
softwares. I read the manuals and am a little bit confused on how to
use them.

I have 2 sequence files
1.  abc_F.abi  - forward read i.e read from 5' to 3' on the sense
strand and the other is,
2.  abc_R.abi  - reverse read i.e read from 5' to 3' on the antisense
strand.



I need to create a contig of these two sequences.
These are the following steps I performed.

1)
I used phred and created the following files

abc_F.abi.seq
abc_F.abi.qual
abc_R.abi.seq
abc_R.abi.qual

2) I used the following cross_match commands
cross_match abc_F.abi.seq  vector -screen > screen.out
cross_match abc_R.abi.seq  vector -screen > screen.out

where vector is the name of the sequence file of the vector in the
fasta format .
I got the following output files

abc_F.abi.seq.screen
abc_R.abi.seq.screen

3) I have confusion in using phrap.

My first doubt is how to assemble the above 2 sequences using phrap.

Should I write both the sequences in tht single file?

What should be the naming convention of the file?

Can I get a brief description on how to use phrap. the phrap
documentation is confusing and I am not able to understand.

Can anybody help me?

bye,
LT



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