From 39f23adf9851316686aa67553dc32a870b3245db Mon Sep 17 00:00:00 2001
From: Veronique Legrand <vlegrand@pasteur.fr>
Date: Tue, 31 May 2022 15:18:47 +0200
Subject: [PATCH] updated man
---
doc/rock.pod | 8 +++++---
1 file changed, 5 insertions(+), 3 deletions(-)
diff --git a/doc/rock.pod b/doc/rock.pod
index ac7d24f..ab1ec03 100644
--- a/doc/rock.pod
+++ b/doc/rock.pod
@@ -11,7 +11,7 @@
=over 4
-=item B<rock> [B<-h>] [B<-i> F<file>] [B<-o> F<file>] [B<-k> F<k_mer_size>] [B<-q> F<nucl_qual_score_threshold>] [B<-C> F<kappa>] [B<-c> F<kappa_prime>] [B<-l> F<lambda>] [B<-n> F<nb_distinct_k_mer>] [B<-m> F<min_valid_k_mer_per_read>] [Args]
+=item B<rock> [B<-h>] [B<-i> F<file>] [B<-o> F<file>] [B<-k> F<k_mer_size>] [B<-q> F<nucl_qual_score_threshold>] [B<-C> F<kappa>] [B<-c> F<kappa_prime>] [B<-l> F<lambda>] [B<-n> F<nb_distinct_k_mer>] [B<-m> F<min_valid_k_mer_per_read>] [B<-p>] [Args]
=back
@@ -71,6 +71,9 @@ Default is minimum 4.
Indicate the number of distinct k-mers in input fastq files.
This is useful to compute a more appropriate value than the default one for lambda if you have not specified it with -l.
+=item -p
+
+Use this flag to process PE separately; ie, a PE is kept if either PE1 or PE2 is below the maximum coverage and removed if either PE1 or PE2 is below the minimum coverage.
=item -v
@@ -95,8 +98,7 @@ B<ROCK> is highly parameterizable via its options.
It is possible to refine filtering by adding more criteria:
1) nucleotide score threshold: k-mers containing at least 1 nucleotide below specified threshold will not be taken into account.
2) minimum number of correct k-mers : let X be this number. Reads containing less than X k-mers without nucleotides below threshold will not be processed.
- They will be put in files named with .undefined extension.
- 3) Pair end reads are processed as single.
+ 3) Pair end reads are processed as single or separately.
It is possible to specify the size of the count min sketch by:
1) indicating the number of arrays that you want in it (via the -l option),
--
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