Sort & Index Sam-Files Automatically

Question: Sort & Index Sam-Files Automatically

7.7 years ago by

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

alignment bowtie • 1.6k views

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modified 7.7 years ago by Jim Robinson • 150 • written 7.7 years ago by Jochen Seggewiß • 30

7.7 years ago by

Jim Robinson • 150

Jim Robinson • 150 wrote:

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

ADD COMMENT • link written 7.7 years ago by Jim Robinson • 150

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:

ADD REPLY • link written 7.7 years ago by Jochen Seggewiß • 30

Jo, Use the SAM Tools SAM-TO-BAM tool in Galaxy to convert your SAM file to a BAM file. Ryan -- CONFIDENTIALITY NOTICE: This email communication may contain private, confidential, or legally privileged information intended for the sole use of the designated and/or duly authorized recipient(s). If you are not the intended recipient or have received this email in error, please notify the sender immediately by email and permanently delete all copies of this email including all attachments without reading them. If you are the intended recipient, secure the contents in a manner that conforms to all applicable state and/or federal requirements related to privacy and confidentiality of such information.

ADD REPLY • link written 7.7 years ago by Ryan Golhar • 80

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