To search for reads by name, open the search panel and select
Search for reads by name from the first drop down list. The second drop down list determines whether or not the search will look through all contigs for matches, or just the currently loaded contig. Enter your search term in the combo box - this combo box stores your previous search terms, so it is easy to select a previous search - then click the search button. The table below the controls should fill in with any results. Click on a result to have that read highlighted in the main display.
When searching for reads by name it is possible to specify that the search should use java regular expressions. When regular expressions aren’t being used the search will only find results that match the search term exactly. When regular expressions are being used the search is attempting to match read names to the regular expression provided in the search combo box. As a simple example imagine some reads are prefixed with an identifier. To find all the reads prefixed with that identifier you would enter “prefix.*” (without the quotes) into the search box and carry out the search. Further details on the regular expression syntax used by Table can be found here.
Searching for subsequences¶
To search for subsequences of nucleotide data within either the reads, or the consensus / reference sequence select either
Search for subsequences or
Search in consensus / reference from the first drop down list. The second drop down list determines whether or not the search will look through all contigs for matches, or just the currently loaded contig. Enter your search term into the combo box and click the search button. Once the search is complete the table below will fill in with the results. Click on a result to jump to and highlight the subsequence in the read or consensus / reference.
When searching for subsequences the option to
Ignore pads when searching is available. This means that pads in the nucleotide sequences will be ignored when trying to match against the search string. Ns are also skipped when this option is selected, this means that for example the search term ACGT will match the following sequences: