ERANGE mRNA counts problem

[yh253]

Hi,

I use ERANGE for some single end RNA-seq data. I generated all the pre-request files without problem and did the alignment with bowtie. When I am trying to do the rna counts by using geneMrnaCounts.py, the number of multi reads doesn't agree with the actual number of multi reads in my alignment file, although the numbers of unique reads to genome and splices are consistent. I don't understand why the number of multi reads got reduced during the rna counting?

Here goes some details:

Reads statistic from alignment file or rds.log

3966406 unique reads
746951 multi reads
355046 spliced reads

$python /Users/commoncode/geneMrnaCounts.py hsapiens s_1.rds s_1_uniqs.count -markGID -cache 1
/Users/commoncode/geneMrnaCounts.py: version 5.1
marking GID and NM
caching ....
dataset RDS/s_1_scr2.rds
metadata:
bowtie_mapped True
dataType RNA
paired True
rdsVersion 1.1
readsize 30
spacer 2

3966406 unique reads, 355046 spliced reads and 677632 multireads
default cache size is 1000000 pages
found index
getting gene features....
getting geneIDs....
Flagging all reads as NM
....
....
....

Appreciate very much for your help!!