rsem v1.1.12 extract-transcript-to-gene-map-from-trinity changed

[rsem.git] / rsem-calculate-expression

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 93fabce4686c8d0b7e4fafeae279c6262e7d412e..9b4e69ea0d47ce19ee292b9e4b6f073e6891c1b7 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -484,7 +484,7 @@ Calculate 95% credibility intervals and posterior mean estimates.  (Default: off
 
 =item B<--seed-length> <int>
 
-Seed length used by the read aligner.  Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads.  If RSEM runs Bowtie, it uses this value for Bowtie's seed length parameter.  (Default: 25)
+Seed length used by the read aligner.  Providing the correct value for this parameter is important for RSEM's accuracy if the data are single-end reads.  If RSEM runs Bowtie, it uses this value for Bowtie's seed length parameter. The minimum value is 25. (Default: 25)
 
 =item B<--tag> <string>
 
@@ -624,7 +624,7 @@ Only generated when --out-bam is specified.
 genomic coordinates. Alignments of reads that have identical genomic
 coordinates (i.e., alignments to different isoforms that share the
 same genomic region) are collapsed into one alignment.  The MAPQ field
-of each alignment is set to max(100, floor(-10 * log10(1.0 - w) +
+of each alignment is set to min(100, floor(-10 * log10(1.0 - w) +
 0.5)), where w is the posterior probability of that alignment being
 the true mapping of a read.  In addition, RSEM pads a new tag
 ZW:f:value, where value is a single precision floating number