MIRA3 multiple input files from same tech

[grassgirl]

Hello,

I am interested in doing a MIRA assembly with two sets of reads from two separate 454 runs. I am wondering if I can feed the runs individually, i.e., post both fastas with related qual files as long as I have unique prefixes. For example:

First set: vh_in_1.454.fasta and vh_in_1.454.fasta.qual

Second set: vh_in_2.454.fasta and vh_in_2.454.fasta.qual


Or do I need to combine the reads and their relative qual files before running an assembly?

[maubp]

I think you need to combine them.

P.S. MIRA will accept a single FASTQ file rather than a paired FASTA + QUAL, which I personally find much easier to work with.

[grassgirl]

Yeah, I can do the fastq approach, but the files come from the sequencing service as SFF, reads, and qual. So I'd either have to extract the fastq from SFF or combine the reads and qual files. Just being lazy I suppose trying to use what is already supplied

[sklages]

MIRA will accept both a single fastq file or a single fasta file with its corresponding qual file.
Just concat either of them. Just one input file per technology :-)

You might want to have a look at sff_extract (http://bioinf.comav.upv.es/sff_extract/usage.html).

[grassgirl]

sklages, thank you for the info. You're right, I could go back and extract the fastq file and then do the clipping, but it already comes clipped from our sequence service, so I will avoid reinventing the wheel and do the concatenate route...which I found pretty quick and easy via the unix 'cat' command.

Thanks for letting me know about the 1-file restriction.

[BaCh]

Thanks for letting me know about the 1-file restriction.

That restriction is about to fall in the next development release of MIRA.

B.

[grassgirl]

Thanks B. I was thinking of suggesting that as an upgrade, but it seems it is already in the works. That will be great.

gg.