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  • ERANGE mRNA counts problem

    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!!

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