Changes between Version 24 and Version 25 of SOPs/qc_shortReads

Timestamp:

04/28/16 14:56:49 (9 years ago)

Author:

thiruvil

Comment:

--

SOPs/qc_shortReads

@@ -220 +220 @@
 Many functions \\
 
-= Analyzing potential species composition of reads in a fastq file =
+= Analyzing potential species composition/contamination 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.
@@ -226 +226 @@
    * 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.
    * FastQ Screen uses bowtie or bowtie2 for mapping. The libraries you wish to screen against need to be bowtie-indexed.
-   * Paths to the bowtie indexed libraries need to be specified in the fastq_screen.conf file, which is called either from the same directory where the fastq_screen program is (by default) or from a manually specified location using the -conf /path/to/.conf file optioin.
+   * Paths to the bowtie indexed libraries need to be specified in the fastq_screen.conf file, which is called either from the same directory where the fastq_screen program is (by default) or from a manually specified location using the -conf /path/to/.conf file option 
    * Sample commands are:
 {{{
 
-"bsub fastq_screen [OPTION] file.fq"
+Usage: fastq_screen [OPTIONS] file.fq
+eg. fastq_screen --aligner bowtie2 myFastQ.txt
 
    Commonly used options are:
@@ -237 +238 @@
    [--outdir]        Specify a directory in which to save output files.
    [--illumina1_3]   Assume that the quality values are in encoded in Illumina v1.3 format. Defaults to Sanger format if this flag is not specified.
-   [--conf]          Manually specify a location for the configuration file to be used for this run. If not specified then the file will be taken from the same directory as the fastq_screen program.
+   [--conf]          Manually specify a location for the configuration file to be used for this run. If not specified then the file will be taken from the same directory as the fastq_screen program. Note: the config file is already setup on our internal server
 
 }}}