@@ -148,7+148,8 @@ The plots generated depends on read type and user configuration. It
may include fragment length distribution, mate length distribution,
read start position distribution (RSPD), quality score vs observed
quality given a reference base, position vs percentage of sequencing
may include fragment length distribution, mate length distribution,
read start position distribution (RSPD), quality score vs observed
quality given a reference base, position vs percentage of sequencing
-error given a reference base and histogram of read alignments.
+error given a reference base and histogram of reads with different
+number of alignments.
fragment length distribution and mate length distribution: x-axis is fragment/mate length, y axis is the probability of generating a fragment/mate with the associated length
fragment length distribution and mate length distribution: x-axis is fragment/mate length, y axis is the probability of generating a fragment/mate with the associated length
@@ -158,7+159,7 @@ Quality score vs. observed quality given a reference base: x-axis is Phred quali
Position vs. percentage sequencing error given a reference base: x-axis is position and y-axis is percentage sequencing error
Position vs. percentage sequencing error given a reference base: x-axis is position and y-axis is percentage sequencing error
-Histogram of read alignments: x-axis is the number of alignments a read has and y-axis is the number of such reads
+Histogram of reads with different number of alignments: x-axis is the number of alignments a read has and y-axis is the number of such reads. The inf in x-axis means number of reads filtered due to too many alignments
-barplot(pair[,2], names.arg = pair[,1], xlab = "Number of Alignments", ylab = "Number of Reads", main = "Histogram of Read Alignments")
+barplot(pair[,2], names.arg = pair[,1], xlab = "Number of Alignments", ylab = "Number of Reads", main = "Histogram of Reads with Different Number of Alignments")