To sequence trim reads
You use the Sequence trim function to trim sequence reads within a .fasta or .fastq file, with or without using quality scores. For example, you can trim unwanted bases at the ends of reads, such as the first color call of SOLiD System reads or barcode tags. You can also trim reads relative to the number of “N” calls. Low quality reads can also be trimmed from a sample if a specified number of bases at the 3’ end falls below a set threshold.
1. In the Input pane, click Add to browse to and select the .fasta file or .fastq file for which the sequence reads are being trimmed.
2. In the Output field, you can leave the default value for the location of the output files as is (the default value is the directory path for the input file), or you can click Set to select a different location.
3. Select the options for filtering and trimming low quality reads.
Setting | Description |
|---|---|
Remove 5’ [ ] Bases and 3’ [ ] Bases | Select this option to remove a set number of nucleotides from the 5’ end of a sequence, the 3’ end of a sequence, or both ends of a sequence. |
Max # of Uncalled Bases >= | Select this option to remove entire reads from the sample file when the file contains more N calls than specified. |
Called Base Number of Each Read | Select this option to remove entire reads from the sample file when the total number of called bases is less than the specified threshold. |
Trim 3’ End while >= [ ] Base(s) with Score <= [ ] | Select this option to trim the 3’ end of a read if the specified number of consecutive bases falls below a set quality threshold score. Note: For additional information about how this option works, see Trim or Reject Read While >= [x] Bases with Score <= [y]. |
Saved the Trimmed Reads/Qual in One Line | Select this option to save trimmed files with each read in a single line. Note: This prevents longer reads being divided into multiple lines. |
Trim By Sequences | Select this option to trim reads where the specified sequence occurs. |
Trim by Sequences in the File | Selected by default. Load a text file that contains the sequences by which the reads are to be trimmed. See Trim by sequences in the file. |
4. Optionally, if you selected Trim by Sequences or Trim by Sequences in the File, click Advanced Settings to open the Advanced Settings dialog box and select the advanced settings by which trim the sequences.
5. Optionally, before you process the files, click Save to save the settings that you have specified to a Settings file (.ini file).
 | You can always load this file at a later date and process other data files according to the saved settings in the file. |
6. Click OK.
A message opens when the process is completed. Depending on the options that you have selected, up to two files are produced—one with trimmed reads and one with removed reads—as shown in the figure below. In addition, if a .qual file was used, two more files are produced—a trimmed .qual file and a removed .qual file.
Sequence Trim files
