Bowtie on Galaxy - multiple amplicon sequences instead of reference genome

[vl80]

I am trying to use Bowtie in Galaxy via the web GUI to align Miseq generated amplicons. Our amplicons are from a multiplex PCR and thus instead of a single reference sequence we have a number of (27 to be exact) short sequences (250 - 400 bp) as the references. Now the products can align against any of these, so in the ideal situation I need to be able to upload a sigle file with all the different sequenes and then after alignment generate a table to say how many reads were aligned agaist which sequence. I tried to do this but get a failure message in Galaxy. Is it possible for this to be done or do I need to creat a file where all the sequences are strined together?
Thanks a advance.

[GenoMax]

Did you do it this way? http://wiki.galaxyproject.org/Learn/CustomGenomes

[vl80]

My ref sequences are in FASTA formates with compatible lengths per line
However the file is something like

>Ref_amplicon1
AAAACCGGTTTAA
>Ref_amplicon2
GGTTCCAAAAAA
>Ref_Amplicon3
CCCTTGGAAA

I am not sure if this would be an acceptable form

[GenoMax]

That format should be fine.

The failure message is for what step? Is the alignment failing or something else?

[vl80]

Actually, alignment went OK, my mistake in posting.
When I wanted to convert SAM-BAM an error came. Also, I tried to filter the alined SAM data, the number of sequences remaining in the end were very low by just using the paird reads flag only. Our service provider used bow tie script based method and gave summary tables to us, which showed a high percentage of aligned reads!, Not sure where things go wrong.

[vl80]

This is the error I get on trying to get the coverage stats...

An error occurred with this dataset: Picked up _JAVA_OPTIONS: -Djava.io.tmpdir=/space/g2main [Thu Apr 04 12:10:28 EDT 2013] net.sf.picard.sam.CreateSequenceDictionary REFERENCE=/space/g2main/tmp-gatk-dbNNN9/gatk_input.fasta OUTPUT=/space/g2main/tmp-gatk-dbNNN9/dict7890443155236506554.tmp

[GenoMax]

Are you using the main galaxy site or a local mirror?

[vl80]

I am using the Galaxy site at https://main.g2.bx.psu.edu/ Not a locally downloaded version..

[GenoMax]

Have you posted to the galaxy help list ([email protected])? They are very helpful and prompt to respond.

[vl80]

Yes I did, unfortunately no reply yet. I tried to send an error message too. Still no feed back.