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.
Unfortunately, In my opinion, there seems to be no proper way to achieve your goal. but if you want to map your fastq file to reference genome , BWA is a nice choice
Blast is Ok but I am not sure if you know what you want to do? it would be better if you read some basics and learn the purpose of sequence analysis.
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