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lib/App/SimulateReads/Command/Custom.pm  view on Meta::CPAN

=item B<--id>

Overlap the default defined template id:
I<single-end> %i.%U %U and I<paired-end> %i.%U %U
e.g. SR123.1 1
See B<Format>

=item B<Format>

A string B<Format> is a combination of literal and escape characters similar to the way I<printf> works.
That way, the user has the freedom to customize the fastq sequence identifier to fit her needs. Valid
escape characteres are:

Common escape characters

	Escape       Meaning
	------       ------------------------------------------
	%i   	     instrument id composed by SR + PID
	%I           job slot number
	%q           quality profile
	%e           sequencing error
	%R           read 1, or 2 if it is the paired-end mate
	%U           read number
	%r           read size
	%c           sequence id as chromossome, ref
	%s           read or fragment strand
	%t           read start position
	%n           read end position

Paired-end specific escape characters

	Escape       Meaning
	------       ------------------------------------------
	%T           mate read start position
	%N           mate read end position
	%D           distance between the paired-reads
	%m           fragment mean
	%d           fragment standard deviation
	%f           fragment size
	%S           fragment start position

lib/App/SimulateReads/Command/Genome.pm  view on Meta::CPAN

=item B<--id>

Overlap the default defined template id:
I<single-end> %i.%U_%c_%s_%t_%n and I<paired-end> %i.%U_%c_%s_%S_%E
e.g. SR123.1_chr1_P_1001_1101
See B<Format>

=item B<Format>

A string B<Format> is a combination of literal and escape characters similar to the way I<printf> works.
That way, the user has the freedom to customize the fastq sequence identifier to fit her needs. Valid
escape characteres are:

Common escape characters

	Escape       Meaning
	------       ------------------------------------------
	%i   	     instrument id composed by SR + PID
	%I           job slot number
	%q           quality profile
	%e           sequencing error
	%R           read 1, or 2 if it is the paired-end mate
	%U           read number
	%r           read size
	%c           sequence id as chromossome, ref
	%s           read or fragment strand
	%t           read start position
	%n           read end position

Paired-end specific escape characters

	Escape       Meaning
	------       ------------------------------------------
	%T           mate read start position
	%N           mate read end position
	%D           distance between the paired-reads
	%m           fragment mean
	%d           fragment standard deviation
	%f           fragment size
	%S           fragment start position

lib/App/SimulateReads/Command/Transcriptome.pm  view on Meta::CPAN

=item B<--id>

Overlap the default defined template id:
I<single-end> %i.%U %U and I<paired-end> %i.%U %U
e.g. SR123.1 1
See B<Format>

=item B<Format>

A string B<Format> is a combination of literal and escape characters similar to the way I<printf> works.
That way, the user has the freedom to customize the fastq sequence identifier to fit her needs. Valid
escape characteres are:

Common escape characters

	Escape       Meaning
	------       ------------------------------------------
	%i   	     instrument id composed by SR + PID
	%I           job slot number
	%q           quality profile
	%e           sequencing error
	%R           read 1, or 2 if it is the paired-end mate
	%U           read number
	%r           read size
	%c           sequence id as chromossome, ref
	%s           read or fragment strand
	%t           read start position
	%n           read end position

Paired-end specific escape characters

	Escape       Meaning
	------       ------------------------------------------
	%T           mate read start position
	%N           mate read end position
	%D           distance between the paired-reads
	%m           fragment mean
	%d           fragment standard deviation
	%f           fragment size
	%S           fragment start position