SOLiD ma2gff

[jlli]

Does anyone have experience with SOLiD GFF Conversion Tool (ma2gff)? I downloaded MaToGffSRC.0.2.04.zip from SOLiD software web site, but it is difficult to install it into unix.

Many thanks,

[Rao]

Use GFF tool from small RNA tool...

[Mr Mutundes]

Yes, the installation instructions seem to be AWOL. FWIW this is what I did to install it:

- make sure ant (http://ant.apache.org/) is installed

- update JDK to 1.6Java SE Development Kit (JDK) 6 Update 11

- make sure the directory /share/apps/corona exists, or else edit this line in build.xml:
<property name="corona.root.dir" location="/share/apps/corona"/>
to reflect the directory you want (I used /usr/share/apps/corona)

- in a suitable directory do:
unzip unzip MaToGffSRC.0.2.04.zip

- run ant:
ant -p
shows all the build targets, and of these "dist-corona" seemed appropriate, so do:
ant dist-corona

- make newly-installed shell scripts executable:
chmod +x /usr/share/apps/corona/bin/*sh

- add /usr/share/apps/corona/bin to your path eg. in bash do:
export PATH=/usr/share/apps/corona/bin:$PATH

That worked for me - hope it helps!

[lellabioinfo]

Dear All, I'm a beginner in bioinformatic analysis of next generation data.
I have a problem with *.csfasta.ma and *csfasta_extend.ma files. I have to align this sequence to a reference genome to detect SNPs or other mutations. But all the programs that allow the alignment, want in input gff or fasta file. So how can i do to convert my file to these format? I have many difficulties using MaToGff tool (for the installation) and in the RNA Pipeline Tools I can't find a tool for my objective.
The other question is about the Small RNA Pipeline Tool from ABI. How can I find filter_step_reference_file, miRBase_step_reference_fasta_file; miRBase_step_reference_fasta_file; genome_step_reference_fasta_file?
Thanks a lot for you attention and for your help,
Best Regards

[nilshomer]

Dear All, I'm a beginner in bioinformatic analysis of next generation data.
I have a problem with *.csfasta.ma and *csfasta_extend.ma files. I have to align this sequence to a reference genome to detect SNPs or other mutations. But all the programs that allow the alignment, want in input gff or fasta file. So how can i do to convert my file to these format? I have many difficulties using MaToGff tool (for the installation) and in the RNA Pipeline Tools I can't find a tool for my objective.
The other question is about the Small RNA Pipeline Tool from ABI. How can I find filter_step_reference_file, miRBase_step_reference_fasta_file; miRBase_step_reference_fasta_file; genome_step_reference_fasta_file?
Thanks a lot for you attention and for your help,
Best Regards

You should have csfasta and csfastq input files in you "primary" directories. You can then use BFAST or MAQ to convert these to FASTQ file(s).

[lellabioinfo]

Thank you very much, but this is the problem! I have available only the *ma file in my directories!

[Rao]

I think you are using RNA pipeline... there is a option to generate GFF files

[Rao]

Also there compiled MaToGff tool available from the same site

[lellabioinfo]

Thanks so much to both of you. I knew the MaToGff tool from ABI but it's too difficult to install it. And in the RNA_pipeline (from ABI), I can't find the option to generate GFF files.
As an alternativa, are there any alignment browsers that use as input *ma files?

[lellabioinfo]

Ok. I installed MaToGff successfully (with difficulty), by follow the directions given by Mr Mutundes (thanks a lot) with the Corona_lite pipeline.

When I run the *sh scripts (MatesToGff or MaToGff for example), as
> MaToGff.sh reads.csfasta.ma.25.2 --convert=unique --clear=1 --sort --qvs=reads.qual > _gff_temp_

the program return me this error:

[: 21: ==: unexpected operator
/usr/share/apps/corona/bin/MaToGff_module.sh: 17: Syntax error: "(" unexpected

But I controlled the file and there is not syntax error.

Has someone else found the same problem?

[mmorley]

Ok. I installed MaToGff successfully (with difficulty), by follow the directions given by Mr Mutundes (thanks a lot) with the Corona_lite pipeline.

When I run the *sh scripts (MatesToGff or MaToGff for example), as
> MaToGff.sh reads.csfasta.ma.25.2 --convert=unique --clear=1 --sort --qvs=reads.qual > _gff_temp_

the program return me this error:

[: 21: ==: unexpected operator
/usr/share/apps/corona/bin/MaToGff_module.sh: 17: Syntax error: "(" unexpected

But I controlled the file and there is not syntax error.

Has someone else found the same problem?

Yep have the same problem but I cannot seem to get past it... Has anyone gotten this to work?

[Mr Mutundes]

wild guess - it's the same problem as reported here:

http://ubuntuforums.org/archive/index.php/t-631680.html

So worth a try running your command like this:

bash /path/to/MaToGff.sh reads.csfasta.ma.25.2 --convert=unique --clear=1 --sort --qvs=reads.qual > _gff_temp_

Of course you need to give the proper path to specifiy the location of MaToGff.sh (e.g. /usr/share/apps/corona/bin/MaToGff.sh)

[mmorley]

With Ubuntu Hardy this did not work:

bash $CORONAROOT/bin/MaToGff.sh

I however installed on RHEL box and works fine.

[westerman]

"Mr Mutundes" has the correct answer -- Ubuntu by default uses 'sh' instead of 'bash'. It is not enough to run the first command -- MaToGff.sh -- via bash since that command calls the second command -- MaToGff_module.sh -- which will run under 'sh'. You need to modify both programs to use 'bash'.

[JDS]

lellabioinfo, you can use MaToGff to convert the extend.ma file into GFF, and then run Annotation Changes to convert the color space seqence into base sequence, remember that you have to write a script by yourself to cut the length of each reads ( display in the extend.ma file of each matched reads), then you can get a fasta file contains all base string of matching reads.

you can get the files in the following way.
filter_step_reference_file : by yourself, put all seq you don't want, rRNA, tRNA or more, in fasta format.
miRBase_step_reference_fasta_file : you can ask the pipeline to create for you at the first run.
miRBase_step_reference_gff_file : download from sanger. genome_step_reference_fasta_file : download somewhere, but HAVE TO MAKE SURE this file should coordinate with the miRBase_step_reference_gff_file.

Read the documentation before the run.

Hope this can help.