Question: Quality check of sequences in fasta format
0
gravatar for Fid_o
10 months ago by
Fid_o20
Fid_o20 wrote:

Hello,

I have .FASTA files of bacterial genomes. I want to check quality of the sequences. Which program accepts quality analysis of .FASTA files?

Cheers!

alignment assembly genome • 510 views
ADD COMMENTlink modified 10 months ago by GenoMax96k • written 10 months ago by Fid_o20

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.

ADD REPLYlink modified 10 months ago • written 10 months ago by GenoMax96k

@genomax, I mean to check the quality like we would check using FASTQC. I realise FASTQC takes in Fastq files, I have .FASTA files.

ADD REPLYlink written 10 months ago by Fid_o20

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?

ADD REPLYlink modified 10 months ago • written 10 months ago by GenoMax96k

@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.

ADD REPLYlink written 10 months ago by Fid_o20
1

can I safely convert fasta files to fastq for purpose of FASTQC use?

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?

ADD REPLYlink modified 10 months ago • written 10 months ago by GenoMax96k

@genomax. Thank you for your replies. I needed quality check for my SNP analysis on these sequences.

ADD REPLYlink written 10 months ago by Fid_o20
1

Not much you can do if you just have fasta sequence. Look for multiple reads (bases) supporting a particular call.

ADD REPLYlink written 10 months ago by GenoMax96k

Thank you for that help and insight. Absolutely helpful.

ADD REPLYlink written 10 months ago by Fid_o20
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