Bowtie output file help

[jpmatteson]

I'm using bowtie to do alignments, the index is made from 96 bacterial genomes, some genomes are incomplete and composed of many contigs. The fasta index files for the contigs are broken up by lines that label each contig, like contig0001, etc. followed by ATCG..., I have the individual index files labeled by SVID# and want the file name (SVID#) reported not the contig0001 part. Is there a way to get the file name to output rather than the contigs from that file?

Could it be that, in the text file, breaking up lines of ATCG... with contig001, contig002, etc... that bowtie reads these as separate files instead of one whole file? any input would be much appreciated!

Thanks