[asifemon]

[QUOTE=bio-x;6068]

usage: $0 [options] -l libraryname -s seq.fasta -q qlt.fasta > new.frg

can someone give me a complete exampe to run this command.

[sklages]

Probably,

convert-fasta-to-v2.pl

taken from resource mentioned above ..

cheers,
Sven

[dan]

usage: $0 [options] -l libraryname -s seq.fasta -q qlt.fasta > new.frg

What is $0 ?

[bio-x]

hi, you can try the following,

usage: $0 [options] -l libraryname -s seq.fasta -q qlt.fasta > new.frg
-v vector-clear-file A file of 'readUID vecBeg vecEnd', one per line, that is the vector clear range.
-noobt Set the 'doNotOverlapTrim' library feature.
-454 Set library features appropriate for 454 reads (see also sffToCA).
-idregex pattern Use this perl regex to extract the read name from the seq defline.
-l libraryname Name of the library; freeformat text.
-mean m Insert has mean size of m.
-stddev s Insert has std dev of s.
-s seq Fasta file of sequences.
-q qual Fasta file of quality values.
-m matepairing A file of pairs of read UIDs for mated reads, one pair per line, whitespace separated

[dan]

Cheers Sven,

That looks like a great resource!


Dan.

[sklages]

@gengen,

Have a look at Celera Input Formatting

Sven

[novice2]

To all members

I have attached a further 2 images showing this effect.

[novice2]

To all members

Dear All

My pcr assay has suddenly began producing these curious strutures-- I have attached an image to show this effect. Can anyone explain please what mat be going on and what I can do to get rid of it. Before this the pcr was working fine.

[gengen]

How to create frg file from SRA data ?

I want to run Celera Assembler usign SRA 454 data, but SRA doesn't provide sff data. They only provide FASTA and FASTQ.
So, how should I do ? I could do this by coverting FASTQ to FASTA and quality file and then converting them to frg file, but this is so roundabout and also I must write some scripts. Let me know if you have any idea for this issue.

thanks in advance

[dan]

Are you planning to use the Celera assembler with short reads? Because I don't think it would work very well.

Have a look here,

http://seqanswers.com/forums/showthread.php?t=719&highlight=celera

[sklages]

pair    \W+\.b\.abi    \W+\.g\.abi

If this is a perl RE "\W+" means, "everything but chars, digits and _"; that is
probably not what you want.

Your sample name looks like this: 065I03X00001.b.abi

better this way (\t as separator):

 pair  (.*)\.b\.abi$ (.*)\.g\.abi$

hth,
Sven

[dan]

I should try before I reply... Setting test.mates to

pair	\.b\.abi	\.g\.abi

Seems to have had the desired effect!

Now I just need to rerun the assembly and check in hawkeye.

[dan]

Sadly it doesn't seem to be working...

toAmos -s x.fasta -q x.qual  -o a.afg

toAmos -s x.fasta -q x.qual -m test.mates -o b.afg

Gives:

diff a.afg b.afg
5c5
< Thu Dec  4 12:24:40 2008
---
> Thu Dec  4 12:27:07 2008

Following the info on the link I set test.mates to the following:

pair	\W+\.b\.abi	\W+\.g\.abi

Their is no error on either command.

[sklages]

Yeah, that's what I wanted to send just about now

http://amos.sourceforge.net/docs/bambus/Manual.html#matesfile

Btw,. I meant Bambus *input* not output ...

cheers,
Sven

[dan]

Seems the Bambus docs will help:

http://amos.sourceforge.net/docs/bambus/Manual.html