I have some amplicon sequences for 144 samples that I would like to map on to a reference gene to identify SNPs. For this I am planning on using Bowtie2 in galaxy for the mapping part and then use Sams tools- mpileup for the snp calling. My question is that i am currently struggling to map multiple fastq files simultaneously with Bowtie2, it only lets me done one at a time. Can I map multiple input fastq file with Bowtie2 in galaxy instance?
Thank in advance for the help!