www.gusucode.com > bioinfo 案例源码程序 matlab代码 > bioinfo/TrimSequencesInAFASTQFileExample.m
%% Trim sequences in a FASTQ file % %% % Trim each sequence when the number of bases with quality below 20 is % greater than 3 within a sliding window of size 25. % [outFile,nt,unt] = seqtrim('SRR005164_1_50.fastq', 'Method', 'MaxNumberLowQualityBases', ... 'Threshold', [3 20], 'WindowSize', 25); %% % Check the number of sequences that were trimmed. nt %% % Check the number of sequences that were untrimmed. unt %% % Trim the first 10 bases of each sequence. % % [outfile,nt] = seqtrim('SRR005164_1_50.fastq','Method','Termini', ... % 'Threshold',[10 0]); % %% % Trim the last 5 bases. % % [outfile,nt] = seqtrim('SRR005164_1_50.fastq','Method','Termini', ... % 'Threshold',[0 5]); % %% % Trim each sequence at position 50. % % [outfile,nt] = seqtrim('SRR005164_1_50.fastq','Method','BasePositions', ... % 'Threshold',[1 50]); % %% % Trim each sequence when the running average base quality becomes less % than 20. % % [outFile,nt,unt] = seqtrim('SRR005164_1_50.fastq','Method','MeanQuality', ... % 'Threshold',20) % %% % Trim each sequence when the percentage of bases with quality below 10 is % more than 15. % % [outFile,nt,unt] = seqtrim('SRR005164_1_50.fastq','Method','MaxPercentLowQualityBases', ... % 'Threshold',[15 10])