Question: Quality check of sequences in fasta format
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What kind of quality are you referring to?
If it means how "complete" is the genome then there are tools like BUSCO for that purpose.
@genomax, I mean to check the quality like we would check using FASTQC. I realise FASTQC takes in Fastq files, I have .FASTA files.
You can't. Fasta format does not allow for encoding of quality scores.
Note: There is an [fasta/qual format] which basically splits a fastq files into sequence/quality files (used by 454 I think). I don't think that is very prevalent. Do you have files like that by any chance?
@genomax I don't have the fasta/qual files, it's just the fasta files.
This being the case, can I safely convert fasta files to fastq for purpose of FASTQC use? My first reservations with conversion would be possibility of introducing errors to the files.
While you can do that it is meaningless in terms of analysis. You would set an artificial Q scores for each base. BTW, why do you need quality scores for your fasta files?
@genomax. Thank you for your replies. I needed quality check for my SNP analysis on these sequences.
Not much you can do if you just have fasta sequence. Look for multiple reads (bases) supporting a particular call.
Thank you for that help and insight. Absolutely helpful.