alignment reads with genomic reads problem
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Entering edit mode
10 months ago

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??

rna-seq RNA-Seq alignment blastn • 373 views
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Entering edit mode
10 months ago
GenoMax 102k

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.

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