How to do CASAVA alignment by using fastq files

[weasteam]

Hi, I am trying to make CASAVA1.8 work.

The company give me the demultiplexing data (in fastq format), Can some one please let me know how to do the alignment with CASAVA1.8?

I am very confused with all different folders created by CASAVA. can I run casava directly by only input the fastq files and the references? If not, may I know what kind of folder structure should I prepare for it able to process?

Thanks a lot and happy new year!!!

[GenoMax]

If you are getting data in "fastq" format (it is not clear if data is already de-multiplexed or does it need de-multiplexing) is there a specific reason you want to use CASAVA (eland) for alignments?

It may be simple to use standard tools like bwa/bowtie/samtools to proceed with the downstream analysis.

If you do want to run full CASAVA (alignments and down stream SNP-calling etc) then you would need access to the entire folder structure for the flowcell data. This process may be intimidating to learn, specially if this is a one time thing.

You should be able to run just the alignments (with eland) standalone with right reference data files and sample sequence files. The command line options for doing that are described in the manual for CASAVA.

[weasteam]

Thanks GenoMax,

the fastq files are demultiplexed, it should be ready to go.

I am contacting the company to hand me the full "Unaligned" folder. Hopefully, I am able to run it tomorrow.