BLAST fastq file to a custom database

Question

[hellen6570]

Hi all,

I got some fastq files from nanopore and trying to blast to a custom database.

So first, I build a database:

makeblastdb -in sh_general_release_dynamic_02.02.2019.fasta -dbtype nucl -out UniteBlast

Building a new DB, current time: 04/25/2019 15:41:39
New DB name:   /igbgroup/a-m/henganl2/Unite/UniteBlast
New DB title:  UniteBlast
Sequence type: Nucleotide
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 35667 sequences in 1.76276 seconds.

Then, when I try to use -blastn

blastn -query BC15.fastq -db /igbgroup/a-m/henganl2/Unite/UniteBlast -task blastn -outfmt 6 -out BC15_B.xml

I got the following error:

CFastaReader: Hyphens are invalid and will be ignored around line 1`FASTA-Reader: Ignoring invalid residues at position(s): On line 1: 1-5, 7-9, 11, 16, 18-19, 21-24, 26-28, 30-37, 42, 44, 49, 51-60, 62-65, 68-71, 73, 76-77, 79-84, 89-92, 94, 96, 98, 100, 102-103, 106, 109-114, 118-120, 127, 129, 131-136, 138-139, 141-142, 144-152

` Can anyone help me out? Thanks!!

Answer 1

[GenoMax]

You can't use a fastq format file to do blast. Convert to fasta format before doing search. Use reformat.sh from BBMap suite.

reformat.sh in=your.fq out=your.fa

Ideally you should use minimap2 instead of blast+:

Answer 2

[JC]

Blast cannot use Fastq as input, you can convert your file or use MAGIC-Blast instead.