transformatin from bed to gtf

[aquleaf]

Hi.

I'm trying to transform the bed file from Scripture to gtf file, then I can input this gtf file into Cuffcompare. Does anyone know how to transform?

Wish your help! Thanks so much!

[upendra_35]

Try this........

java -Xmx1000m -jar <path_to_scripture>/scripture_alpha2.jar -task toGFF -cufflinks -in your_file.bed -source SCRIPTURE -out your_file.gtf

[bekkari]

hi,
can you please explain in detail, the option you provided here to convert bed to gtf?
especially what do you mean by "path_to_scripture", do we need to download any scripts?
Thanks in advance
java -Xmx1000m -jar <path_to_scripture>/scripture_alpha2.jar -task toGFF -cufflinks -in your_file.bed -source SCRIPTURE -out your_file.gtf

[11xinqi]

Hi.

I'm trying to transform the bed file from Scripture to gtf file, then I can input this gtf file into Cuffcompare. Does anyone know how to transform?

Wish your help! Thanks so much!

Hi, have you tried scripture to transfer bed file to gtf file?

[GenoMax]

I believe upendra_35 was referring to http://www.broadinstitute.org/software/scripture/.

Here is another option to try: https://github.com/CGATOxford/cgat/b...pts/bed2gff.py

[11xinqi]

Hi.

I'm trying to transform the bed file from Scripture to gtf file, then I can input this gtf file into Cuffcompare. Does anyone know how to transform?

Wish your help! Thanks so much!

Hi

Do you know how to transfer bed file form scripture to gtf file. If you know how to do it now, would you please tell me?

[11xinqi]

hi,
can you please explain in detail, the option you provided here to convert bed to gtf?
especially what do you mean by "path_to_scripture", do we need to download any scripts?
Thanks in advance
java -Xmx1000m -jar <path_to_scripture>/scripture_alpha2.jar -task toGFF -cufflinks -in your_file.bed -source SCRIPTURE -out your_file.gtf

Hi

Do you know where can I download the scripture alpha version?

[11xinqi]

I believe upendra_35 was referring to http://www.broadinstitute.org/software/scripture/.

Here is another option to try: https://github.com/CGATOxford/cgat/b...pts/bed2gff.py

I try to download the alpha version of scripture, but can't get it from http://www.broadinstitute.org/software/scripture

[11xinqi]

Try this........

java -Xmx1000m -jar <path_to_scripture>/scripture_alpha2.jar -task toGFF -cufflinks -in your_file.bed -source SCRIPTURE -out your_file.gtf

I tried bed2gff.py. But there is an error shows that import CGAT.Experiment as E
ImportError: No module named CGAT.Experiment. Would you please help me with that

[GenoMax]

I try to download the alpha version of scripture, but can't get it from http://www.broadinstitute.org/software/scripture

Perhaps your local firewall/security rules are blocking the download. I am able to download the jar file from this link.

[11xinqi]

Perhaps your local firewall/security rules are blocking the download. I am able to download the jar file from this link.

Yes, I can download it. But there are only two Beta version- Beta version and Beta version2. Based on the command above-
java -Xmx1000m -jar <path_to_scripture>/scripture_alpha2.jar -task toGFF -cufflinks -in your_file.bed -source SCRIPTURE -out your_file.gtf, I should get scripture alpha version. Do you know where can I get alpha version?

[GenoMax]

Use what you can download now.

Software development proceeds in steps and the names tell you where a particular release of software is in the development cycle (alpha --> beta -> Release Candidate--> final release). http://en.wikipedia.org/wiki/Softwar...ase_life_cycle

[11xinqi]

Use what you can download now.

Software development proceeds in steps and the names tell you where a particular release of software is in the development cycle (alpha --> beta -> Release Candidate--> final release). http://en.wikipedia.org/wiki/Softwar...ase_life_cycle

Thank you very much. Yes, I know that. But there is no toGFF function for Beta version. Do you know any other software can tansfer BED to GFF?

I tried galaxy to do that, but that does not work also. there is a pic that show the result from galaxy. there are two exons for this transcript, but there are only one exon aftrer transformation and the coordinate is also uncorrect.

[GenoMax]

Did you give this a try? https://github.com/CGATOxford/cgat/b...pts/bed2gff.py

[11xinqi]

Did you give this a try? https://github.com/CGATOxford/cgat/b...pts/bed2gff.py

I tried this. But there was an error -Traceback (most recent call last):
File "bed2gff.py", line 49, in ?
import CGAT.Experiment as E
ImportError: No module named CGAT.Experiment.

Do you know what is the problem?