Blast search for multiple fastq files at a time

[Ecotone23]

Hi,

I have hundreds of fastq files and each file contains multiple sequences. Most of the sequences are DNA extracted from vertebrate bloods. With rBlast, I wonder how I can do a blast search for all these files at once and export blast results including percentage identity, coverage, species ID? Is a database of vertebrate sequences needed as the reference for query?

Thank you,

Gabriel

[mhahsler]

Hi,

you will need a database. You can write a simple loop in R that loads a sequence at a time and blasts it. Depending on how good your R knowledge is, you might want to ask someone for help with writing the code.

Best,
Michael

[Ecotone23]

Hi Michael,

Thank you for getting back to me promptly. I wonder if you know any database that contains mammals and birds that I can download and use as my reference for local BLAST retrieval. I am not that good at R, can you provide some R-script examples of the simple loop that automatically load and blast a sequence?

Best,
Gabriel

[mhahsler]

I only worked with bacteria. I do not have R-script examples. You may want to hire someone. It should be straight forward.

Regsrds,
-Michael