Role Of Perl In Sequence Screening Process Using Seqclean

Question

[meghasihag]

I am going to start an EST analysis project. In which sequences will be processed through seqclean. My question is that what is the role of perl in that process.

[SES]

The SeqClean tool is written in the programming language Perl, therefore you will need Perl installed to use it. That is the direct answer to your question, but was there something more specific you were wanting to know?

[meghasihag]

yes.... there is much more i want to know. Have you ever used seqclean because i am using seqclean for screening of EST sequences of cotton boll and get stuck at a point i don't know i am doing it right or not. Can you help me sort it out.

[SES]

Sorry for the late reply. I have used seqclean in the past, so I could help if you can say what the specific problems are. I will also warn that we stopped using seqclean because it was never completely effective at removing vectors, or other contaminants. I switched to using prinseq and cutadapt for most of my trimming needs.

[Michael]

From the README:

There are 2 perl scripts in this package:
seqclean
bin/seqclean.psx

However this is not quite correct: there are 2 perl scripts and one module:

Mailer.pm: a /usr/local/bin/perl script text executable
cln2qual:  a /usr/bin/perl script text executable
seqclean:  a /usr/bin/perl script text executable

Rest are binaries called from those scripts via system.

So, the role of perl is to execute those scripts :)

[meghasihag]

ok sir thank you

Answer 1

[Chris Fields]

To run the application?