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  • Collapesed reads in Scripture for transcript assembly

    I hava run Tophat for RNA-seq reads mapping, and want to using Scripture for transcripts assembly. the commands are
    tophat -o ./tophat_out_YPD_1 ./Chr1 ../YPD_l1_1.fq
    tophat -o ./tophat_out_YPD_2 ./Chr1 ../YPD_l1_2.fq
    sed '1,2d' tophat_out_YPD_1/accepted_hits.sam | sort > tophat_out_YPD_1/accepted
    _hits.sorted.sam
    sed '1,2d' tophat_out_YPD_2/accepted_hits.sam | sort > tophat_out_YPD_2/accepted
    _hits.sorted.sam
    java -jar ./scripture-beta.jar -task makePairedFile -pair1 tophat_out_YPD_1/accepted_
    hits.sorted.sam -pair2 tophat_out_YPD/accepted_hits.sorted.sam -out YPD.paired.s
    am -sorted
    cat tophat_out_YPD_1/accepted_hits.sorted.sam tophat_out_YPD_2/accepted_hits.sor
    ted.sam > YPD_all_alignments.sam
    java -jar ./igvtools.jar sort YPD_all_alignments.sam YPD_all_alignments.sorted.s
    am
    java -jar ./igvtools.jar index YPD_all_alignments.sorted.sam
    java -jar ./igvtools.jar sort YPD.paired.sam YPD.paired.sorted.sam
    java -jar ./igvtools.jar index YPD.paired.sorted.sam


    so I got some files like these:
    -rw-r--r-- 1 root root 69219776 11-02 19:31 YPD_all_alignments.sam
    -rw-r--r-- 1 root root 69475267 11-02 19:32 YPD_all_alignments.sorted.sam
    -rw-r--r-- 1 root root 613 11-02 19:33 YPD_all_alignments.sorted.sam.sai
    -rw-r--r-- 1 root root 395434 11-02 19:35 YPD.paired.sam
    -rw-r--r-- 1 root root 398912 11-02 19:36 YPD.paired.sorted.sam
    -rw-r--r-- 1 root root 613 11-02 19:36 YPD.paired.sorted.sam.sai


    I create a file "chromosome.sizes" as
    [root@localhost rna-seq]# more chromosome.sizes
    chr7 906452
    chr6 1297466
    chr5 643605
    chr4 733397
    chr3 1521169
    chr2 1534814
    chr1 782162


    and a sequence file "chr1.fa" in the same directory
    then execute the follow command
    java -jar ./scripture-beta.jar -alignment YPD_all_alignments.sorted.sam -out chr1.scr
    iptureESTest.segments -sizeFile chromosome.sizes -chr chr1 -chrSequence chr1.fa -pairedEnd YPD.paired.sorted.sam


    and got the following infomation:
    Using Version VPaperR3
    Computing weights..... upweighting? false weight: 1.0
    Computing alignment global stats for chromosome chr1
    Has pairs: true
    Has upweighting turned on: false
    Computing weights..... upweighting? false weight: 1.0
    AlignmentDataModel loaded, initializing model stats
    Computing alignment global stats for chromosome chr1
    model stats loaded, initializing model
    Built the model: 0.0 free memory: 177830504
    Loaded chromosome Sequence
    Segmenting accross graph
    Going to get read iterator to make graph with counts
    Got read iterator
    Made it through all reads
    Collapsed reads
    Decollapsed by introns
    Made first graph
    Got extended pieces
    Made second graph
    Done making spliced graph
    Got Simple paths...
    Estimated distribution
    Made path trees
    Done adding paired ends (if available)
    Done getting paths. Total: 0
    Done with local segmentation
    Done setting local rate in graph
    Done scoring paths.


    How can I solve this problem?
    thanks!

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