How to blast a paired end fastq file?
Hello everyone, I have a paired end fastq file and I know that BLAST+ in command line, accepts fasta format. But I don't know how does it work for a paired end fastq file (I mean in two different files R1 and R2). Do I have to interleave them and then convert them to fasta? Or should I concatenate them and convert them to fasta? Or should I treat them as separate files and then convert them to fasta?
Thank you, any help would be appreciated.
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chillchik29 •
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2 answers
You can use fastp to merge it first, then blast the merged reads
See the intro here: https://github.com/OpenGene/fastp#merge-paired-end-reads
Use Magic-Blast
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Why do you wish to BLAST read sequences? Plus, why do you want to BLAST both pairs and all reads?
I already selected these group of reads from all the metagenome sequences by aligning them with bbmap, to the phage_nt db. So before assembling them, I wanted to have a first approach of what I had in the sample by aligning them with BLAST and then export it to MEGAN.
You could save some effort and only convert one end to fasta (
reformat.sh in=R1.fq.gz out=R1.fa) and then BLAST. PE reads are not going to give you much additional information that MEGAN can use.Thank you! I'm going to try that out :)