Changes between Version 19 and Version 20 of SOPs/qc_shortReads

Timestamp:

01/08/16 09:30:54 (9 years ago)

Author:

gbell

Comment:

--

SOPs/qc_shortReads

@@ -264 +264 @@
 Many functions \\
 
-= Analyzing potential composition of reads in a fastq file =
-
-   * To get a quick preview of what genomes/collections of sequences the reads in a fastq file might map to, one can use the FastQ Screen tool.
+= Analyzing potential species composition of reads in a fastq file =
+
+   * To get a quick preview of what genomes/collections (or vectors or other contaminants) of sequences the reads in a fastq file can map to, one can use the FastQ Screen tool.
    * Information about FastQ Screen can be found at this page: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/
    * FastQ Screen allows you to screen your fastq file against a set of libraries, which can be set up to contain the genomes of interest, potential contaminating genomes, vectors, sequencing adaptors, ribosomal RNAs, or other contaminants commonly seen in sequencing experiments. This allows you to see if composition of the reads matches with what you expect and, where the contamination might have come from, if any.