Re: [galaxy-user] Calling SNP's

2011-05-16 Thread Jennifer Jackson
Hello Teja, Exploring the "Pages" tutorials is recommended as many have SNP-specific analysis examples. I am not sure if your data is RNA or DNA or if you have quality scores available, but there are tutorials that cover most common-use cases. http://main.g2.bx.psu.edu/page/list_published I

Re: [galaxy-user] Calling SNP's

2011-05-16 Thread Jennifer Jackson
Hello Teja, If you have a fasta file of sequences, you can map them to a reference genome to obtain a SAM file (which you could then compress into BAM). See the tool section "NGS Toolbox". BLAST is an alignment tool and additional parsing/analysis tools would be needed in order to identify S

[galaxy-user] Calling SNP's

2011-05-13 Thread sukeerthi teja Rallapalli
Hi, Is it possible to convert a fasta file to sam/bam format using galaxy. ? OR Is is possible to call SNP's using Blast 2.2.25 (Stand Alone Blast) Thank you Teja ___ The Galaxy User list should be used for the discussion of Galaxy analysi