How to extract the singletons

[nicedad]

Hi everyone,
Am working with Newbler, which excludes the singletons form the results (454AllContigs etc.)
However, I could only get singletons ID's using SFF tool from 454ReadStatus.txt.
Therefore, my question is, how to extracts singletons (as sequences) from our reads.
As we need to gain an overview about them also.

Does anyone have a script of a tool to achieve this goal.

thanks in advance,

[westerman]

My split reads perl script is enclosed. I never wrote this for public use so it may not work for you. Feel free to modify it as needed.

[nicedad]

Thanks westerman you always have the upperhand.
I'll check it out and get back to you.

best

[nicedad]

westernman, the script could not be ran. can you give an example how to run it.
Unfortunately, once I ran it I got the following massage:

evo-zapus:/opt/454/bin # perl SingletonsFinder.pl

****** Need to run this program on a machine with
with 454 software; e.g., pkr2 or coates. Check for the
program called 'sfffile'. *******

Even though I have sfffile installed and ran several times.
I added 454ReadStatus and 454TrimStatus.txt. in bin directory where sfffile is located

best,

[westerman]

Hum, this is a problem with unpublished and unpolished code. pkr2 and coates are our machines that have the sfffile program on it; thus the message about them. However just before that message is the line:

sfffile --help 2>&1

What happens if you type that command directly at your command prompt?

BTW, feel free to email me directly so that we can get this resolved in a more timely manner. westerman @ purdue dot edu

[wildung]

or there is this shell script in the manual.
from the assemblydirectory:

fgrep Singleton 454ReadStatus.txt > singles.txt
sfffile -o singles.sff -i singles.txt your/path/to/the.sff
sffinfo -s singles.sff > singles.fna

[westerman]

'wildung's response is, as I recall, what my program does. My program also extracts other parts of the file and so is better in an automated pipeline. But those three lines should do exactly what you want without having to get my program to run.

[nicedad]

Thanks guys for the help,
Unfortunately, when I try to run sfffile I get this error even I sat up the class path and when I type the (whereis sfffile) command it turns out the right path
Here is the error:
evo-zapus:/opt/454/bin # sfffile --help 2>&1
If 'sfffile' is not a typo you can use command-not-found to lookup the package that contains it, like this:
cnf sfffile
evo-zapus:/opt/454/bin # cnf sfffiel
sfffiel: command not found

any suggestions?

[nicedad]

Thanks guys, the problem is solved.
I really appreciate this.

regards,