Question: alignment reads with genomic reads problem
gravatar for mxlsherry1992
16 days ago by
mxlsherry199230 wrote:

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??

blastn rna-seq alignment • 87 views
ADD COMMENTlink written 16 days ago by mxlsherry199230
gravatar for genomax
16 days ago by
United States
genomax87k wrote:

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: in=your.fastq out=file.fasta.

ADD COMMENTlink modified 16 days ago • written 16 days ago by genomax87k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 750 users visited in the last hour