Report fastq reads that contain sequences

This tool searches fastq reads for given nucleic acid query sequences. A typical use would be to compare the relative occurrence of two sequences.

NOTE: This only reports complete matches to the sequences, and reads that may partially match at the ends will not be counted.

INPUTS

fastq files

• the sequence files to search

query file - a tabular file

• that contains a column of "query" sequences to match in fastq reads
• it may contain a second "comparison" sequence column to match

OUTPUTS

summary report - a tabular file

• the first column is the line number from the query file
• columns from the query file selected as identifiers
• the count of fastq entries for the query sequence
• the count of fastq entries for the comparison sequence (if selected)
• the fraction of query sequence matches compared to the total of query and comparison matches

count details - an optional tabular file of match count

• the fastq name
• the first column is the line number from the query file
• the sequence that matched
• the label of the sequence that matched
• the strand that matched
• the number reads that matched