If I have a .gff file or a .faa file, how can I use this information to understand what the average length of all the sequences are.
Or is there a program to visualize the distribution of sequence lengths?
Joseph Adelskov
Many NGS quality analysis tools will do this, the PRINSEQ web service is probably the easiest way using a .faa file.
https://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi
Upload your .faa file and run just basic statistics and you'll get some numeric stats and graphical distributions.
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Shabhonam Caim
in linux you can simply do:
awk '{/>/&&++a||b+=length()}END{print b/a}' file.fa
Cheers
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