Select-reads

Overview

select-reads is a tool for selecting a subset of reads from a readbank, along with their fragments and library information. It can also automatically including the mates of reads as well. This tool is especially useful if you need to partition your reads such as when you partition reads according to which plasmid or chromosome they represent.

For example, if you have a list of reads you want to include (reads that align to 1 plasmid) and you want just those reads and their mates use:

select-reads -I plasmida.reads -M read.bnk > plasmida.afg

Now, say you want to print all the reads except for those reads:

select-reads -X plasmida.reads -M read.bnk > notplasmida.afg

Instead, now you have a list of reads that match plasmidb that you want, but you don't want the reads that match plasmida:

select-reads -X plasmida.read -I plasmidb.reads -M read.bnk > plasmidb.afg

Documentation

Synopsis

USAGE: select-reads [options] <bank path>

Print RED, FRG & LIB messages of selected reads from an AMOS Bank

-h            Display help information
-s            Disregard bank locks and write permissions (spy mode)
-v            Display the compatible bank version
-i IIDFile    Specify file containing list of iid's to print
-I EIDFile    Specify file containing list of eid's to print
-L            Just output read names that would be printed by eid
-l            Just output read names that would be printed by iid
-M            Automatically consider mates
-N            Nullify mates in FRG if not printing both mate-pairs
-x IIDFile    File of list reads iids to exclude
-X EIDFile    File of list reads eids to exclude

Notes:

By default, reads are considered independently so you can print a read, but not its mate. The -N option removes references to unprinted mate-pairs in the FRG messages.

In most cases, though, you should use -M to automatically select mates.

You must specify included and/or excluded reads. Precedence is:

1) If a read is excluded by -X or -x, it will not be printed

 (-M) Mates of excluded reads will not be printed either

2) If a read is included by -I or -i, it will be printed except if excluded

 (-M) Mates of included reads will be printed, except if either is excluded
      (Included Reads or mates may be clobbered by excluded reads or mates)

3) If no reads are included, all reads except those excluded will be printed

Exclusion takes precedence over inclusion!