Hi Jo,

To short-circuit confusion I'll jump in here. I'm the developer of IGV and igvtools, the sorting and indexing for SAM files was added long ago, even before indexed BAM files were possible from Java programs. The recommendation now is to convert to BAM and index that, although SAM files still work. If the galaxy community would like the SAM option I'm happy to have igvtools wrapped as a module, and will help with that.

BTW, I also have some code (xml) to wrap IGV itself as a Galaxy visualizer, contributed to me by a user. As I don't have a private Galaxy installation I'm unable to test it myself, but can make it available if anyone is interested.

Jim

Hello!

I convert SOLiD csfasta- and qual-files to fastq-files and map those against Hg19 (Bowtie). I would like to use the resulting sam-files in the IGV browser (Broad Institute). Therefore, the sam-file need to be sorted an indexed. This could be done using the “igvtools”. However, it would be nicer if this sorting and indexing could be done automatically using GALAXY. I guess that it is certainly possible – but I do not know how. Could anybody let me know how it works and what function I have to use, respectively? How can I sort the sam-file the correct way?

Thank you in advance.

Best regards

Jo ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

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Jo,

Use the SAM Tools SAM-TO-BAM tool in Galaxy to convert your SAM file to a BAM file.

Ryan

On 3/25/11 10:35 AM, Jochen Seggewiß wrote:

Hi!

Thank you for your reply.

So that means, I should convert the csfasta & qual to fastq, map it with Bowtie, get an SAM, convert it to BAM and then index that BAM? How can I index BAM using GALAXY? I haven´t found a way to get a BAM directly from GALAXY using csfasta & qual as input files.

Best regards

Jo

Am 3/25/2011 3:13 PM, schrieb Jim Robinson:

...

Hi Jo,

To short-circuit confusion I'll jump in here. I'm the developer of IGV and igvtools, the sorting and indexing for SAM files was added long ago, even before indexed BAM files were possible from Java programs. The recommendation now is to convert to BAM and index that, although SAM files still work. If the galaxy community would like the SAM option I'm happy to have igvtools wrapped as a module, and will help with that.

BTW, I also have some code (xml) to wrap IGV itself as a Galaxy visualizer, contributed to me by a user. As I don't have a private Galaxy installation I'm unable to test it myself, but can make it available if anyone is interested.

Jim

...

Hello!

I convert SOLiD csfasta- and qual-files to fastq-files and map those against Hg19 (Bowtie). I would like to use the resulting sam-files in the IGV browser (Broad Institute). Therefore, the sam-file need to be sorted an indexed. This could be done using the “igvtools”. However, it would be nicer if this sorting and indexing could be done automatically using GALAXY. I guess that it is certainly possible – but I do not know how. Could anybody let me know how it works and what function I have to use, respectively? How can I sort the sam-file the correct way?

Thank you in advance.

Best regards

Jo ___________________________________________________________ The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

---

The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/

---

The Galaxy User list should be used for the discussion of Galaxy analysis and other features on the public server at usegalaxy.org. Please keep all replies on the list by using "reply all" in your mail client. For discussion of local Galaxy instances and the Galaxy source code, please use the Galaxy Development list:

http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists, please use the interface at:

http://lists.bx.psu.edu/