Strategies To Blast Against Fastq Files

Question

[Cacau]

I am going to look for the homolog of my gene in another species using its transcriptome data (Illumina). What might be a good strategy? Is there any tool that can be used to run blast-like search directly against fastq file? I am thinking if it is OK to convert fastq file to fasta format and then run blast. Any help will be appreciated.

Answer 1

[Eric Normandeau]

It is not 100% clear what source of data you want to blast.

Do you want to blast the raw Illumina reads or some form of assembled reads (assembled transcriptome)?

If the former, some tools are fast to blast high volumes of short sequences (blat?), if the latter, then a normal blast would do.

In both cases, going from fastq to fasta is the way the natural way to go. If anybody knows of a blast-like tool that can use fastq, I would be glad to know about it!

Answer 2

[JC]

I will choose to assemble first the transcriptome data with Oases/Trinity/Trans-ABySS and then look for gene homology with blast/blat.

Answer 3

[bioinform_1]

Hi,

I have a nr database, i want to blast fastq (illumina file) on this database, is there any software or anyway?

Thanks

[ctseto]

There's nothing stopping you from stripping the quality lines from a fastq and turning it into a fasta, then running the sequences in blast. Not sure what'd you get out of it asides from a nearest match for each read to a member of your index. Are you trying to count something, map something or assign identities before a de novo assembly? Mapping the reads to the fasta that your nr is derived from might give you visualization of your reads in context of your database if that is what you were looking for.

If your insert length is short enough and your read length long enough, merging reads may give you more to work with; and deduplication may eliminate some reads that correspond to overly represented areas that might save you some runtime.