---+ Using Flexbar program to remove adapter sequences from NGS reads ---++ Installing Flexbar installation instructions coming soon. ---++ Command line usage for removal of adapter sequences Generic conservative command. Replace everything between "" with appropriate names, and delete the "" marks: flexbar -t "New_file_name" -s "read_1_file_name" -p "read_2_file_name" -f fastq -a "fasta_file_of_adapter_sequences" -ao 1 Example command: flexbar -t DED81 -s 02_Downloads/Sample_DED81_L004_R1.cat.fastq -p 02_Downloads/Sample_DED81_L004_R2.cat.fastq -f fastq -a 02_trimmed_Downloads/adapter_seq.fasta -ao 1 For a less conservative command, remove -ao 1 ---++ Flag explanations |*Flag*|*Text to follow*|*What flag means*|*Reason*| |-t|New_file_name|Name of output file.|Dictate what your output file is to be named. Suggest something different than input to avoid overwriting untrimmed.| |-s|R1_source_file_name|Name of Read1 sequencing file.|File to remove adapters from.| |-p|R2_source_file_name|Name of Read2 sequencing file.|File to remove adapters from.| |-f|Format|Format of reads.|Most commonly will be fasta or fastq.| |-a|Adapter_sequence_file.fasta|Fasta file with full adapter sequences, degenerate bases allowed.|What sequence is to be removed.| |-ao|Number|Number of bases of overlap between read and adapter|This number equals the minimum number of bp to be removed.| |-at|Number|Number of mismatches and indels per 10bp of adapter sequence allowed|This accounts for sequencing/PCR errors changing adapter sequence. Default = 3, increasing this number increases false positive rate, and decreases false negative rate.| ---++ Additional Information For additional information, type flexbar -h -- Main.DanielDeatherage - 16 Jan 2013
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Topic revision: r1 - 2013-01-16 - 18:36:01 - Main.DanielDeatherage
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