[galaxy-user] Sort index SAM-files automatically

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

[galaxy-user] Mapping to only 3 genes / targeted resequencing / SOLiD4 / short reads

Hi! Following situation: 10 barcoded samples. Each sample consists of a mix of the sequences 3 independent genes (á 2 alleles). I would like to map the SOLiD4 reads only to the sequences of those 3 genes, patient by patient. First, the 10 barcoded samples have to be separated from each