alignment reads with genomic reads problem

Question

[mxlsherry1992]

Dear all,

I have about 1000 sequences in Fasta format clarias_specific_seq.fasta, and I build a database for that, clarias_speficic_db. I have another Fastq file SRR11188453_1.fastq, I would like to align this Fastq file with the Fasta database, but it reported an error. At first, I thought was due to the large size of Fastq file, but only take two sequences to run a test, I got the same error. Here is the command:

makeblastdb -in clarias_specific_seq.fasta -dbtype 'nucl' -hash_index -parse_seqids -out clarias_speficic_db

blastn -query SRR11188453_1.fastq -db clarias_speficic_db -evalue 1e-5 -num_threads 20 -max_target_seqs 60 -outfmt 6 -out cl_cl_SRR11188453_1.blastout

And here is the reported error:

Error: NCBI C++ Exception:
    "/home/coremake/release_build/build/PrepareRelease_Linux64-Centos_JSID_01_491_130.14.22.10_9052_1363121432/c++/src/objtools/readers/fasta.cpp", line 649: Error: ncbi::objects::CFastaReader::CheckDataLine() - CFastaReader: Near line 1, there's a line that doesn't look like plausible data, but it's not marked as defline or comment. (m_Pos = 1)

If you have any suggestions for that? Or if Align a Fastq file to a Fasta file is not work??

Answer 1

[GenoMax]

You can't use blastn with fastq files. You will need to use magicblast (LINK) instead.

Otherwise convert your fastq files to fasta and then map using blastn. From BBtools suite: reformat.sh in=your.fastq out=file.fasta.