rsem-v1.1.14b3

[rsem.git] / rsem-calculate-expression

diff --git a/rsem-calculate-expression b/rsem-calculate-expression
index 774065a33aced3b9003285be20c52b3cc7017832..cbfef53fd7da453c07c29a5830691933aa8be1fc 100755 (executable)
--- a/rsem-calculate-expression
+++ b/rsem-calculate-expression
@@ -113,9 +113,11 @@ pod2usage(-msg => "Min fragment length should be at least 1!", -exitval => 2, -v
 pod2usage(-msg => "Min fragment length should be smaller or equal to max fragment length!", -exitval => 2, -verbose => 2) if ($minL > $maxL);
 pod2usage(-msg => "The memory allocated for calculating credibility intervals should be at least 1 MB!\n", -exitval => 2, -verbose => 2) if ($NMB < 1);
 pod2usage(-msg => "Number of threads should be at least 1!\n", -exitval => 2, -verbose => 2) if ($nThreads < 1);
-pod2usage(-msg => "Seed length should be at least 25!\n", -exitval => 2, -verbose => 2) if ($L < 25);
+pod2usage(-msg => "Seed length should be at least 5!\n", -exitval => 2, -verbose => 2) if ($L < 5);
 pod2usage(-msg => "--sampling-for-bam cannot be specified if --out-bam is not specified!\n", -exitval => 2, -verbose => 2) if ($sampling && !$genBamF);
 
+if ($L < 25) { print "Warning: the seed length set is less than 25! This is only allowed if the references are not added poly(A) tails.\n"; }
+
 if ($strand_specific) { $probF = 1.0; }
 
 my $mate1_list = "";
@@ -472,7 +474,7 @@ 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. The minimum value is 25. Any read with its or at least one of its mates' (for paired-end reads) length less than 25 will be ignored. (Default: 25)
+Seed length used by the read aligner.  Providing the correct value is important for RSEM. If RSEM runs Bowtie, it uses this value for Bowtie's seed length parameter. Any read with its or at least one of its mates' (for paired-end reads) length less than this value will be ignored. If the references are not added poly(A) tails, the minimum allowed value is 5, otherwise, the minimum allowed value is 25. Note that this script will only check if the value >= 5 and give a warning message if the value < 25 but >= 5. (Default: 25)
 
 =item B<--tag> <string>
 
@@ -560,7 +562,7 @@ One simple way to make the alignment file (e.g. input.sam) satisfying RSEM's req
 
   sort -k 1,1 -s input.sam > input.sorted.sam
 
-The SAM/BAM format RSEM uses is v1.4. However, it is compatible with old SAM/BAM format. 
+The SAM/BAM format RSEM uses is v1.4. However, it is compatible with old SAM/BAM format. However, RSEM cannot recognize 0x100 in the FLAG field. In addition, RSEM requires SEQ and QUAL not be '*'. 
 
 The user must run 'rsem-prepare-reference' with the appropriate reference before using this program.
 
@@ -697,4 +699,3 @@ Assume the path to the bowtie executables is in the user's PATH environment vari
                            mmliver_paired_end_quals
 
 =cut
-