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Added info about output to man page

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1 parent d99e031 commit c2a2f216035f639aade2ec7457d65a11d7d9c4a6 @apmasell apmasell committed Mar 16, 2012
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29 pandaseq.1
@@ -107,6 +107,35 @@ Input files will have their quality encoded as PHRED + 64 instead of the PHRED +
.TP
\-F
Normally, output will be as a FASTA even though per-base quality information is available. To retain this quality information, this flag will output the sequence and the quality information in FASTQ format with quality scores encoded as PHRED + 33. The meaning of the quality score is conceptually different from the input quality scores for the overlap region, but this may not matter depending on your downstream application.
+.SH OUTPUT STATISTICS
+At the end of reconstruction, several statistics are output on lines beginning with \fBSTAT\fR.
+.TP
+READS
+The number of reads in the input files.
+.TP
+NOALGN
+The number of sequences where there exists no overlap with a probability above the threshold.
+.TP
+NOFP
+The number of sequences where the forward primer could not be aligned. This is only done when \fB-p\fR is supplied and a nucleotide sequence.
+.TP
+NORP
+The number of sequences where the reverse primer could not be aligned. This is only done when \fB-q\fR is supplied and a nucleotide sequence.
+.TP
+LOWQ
+The number of sequences where the quality score of the reconstruction (not the quality scores of the individual bases) is below the threshold.
+.TP
+DEGENERATE
+The number of sequences containing uncalled/degenerate/N bases in the final reconstruction (it is immaterial if there are uncalled bases in the reads.) This is only done when \fB-N\fR is provided.
+.TP
+SHORT
+The number of sequences where the final reconstructed sequence is too short. This is only done when \fB-l\fR is provided.
+.TP
+LONG
+The number of sequences where the final reconstructed sequence is too long. This is only done when \fB-L\fR is provided.
+.TP
+OK
+The number of sequences output.
.SH EXAMPLES
This will assemble a data from a run in lane 7:

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