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  • problem with tophat

    Hi, guys. I am completely newbie in this sequencing field.

    I just started using tophat. I installed everything. However, while tophat was mapping my reads, it gave me this error (I am following protocol of tophat and cufflinks- http://www.nature.com/nprot/journal/....2012.016.html)

    My command was:

    $ tophat -p 8 -G genes.gtf -o C1_R2_thout genome C1_R1_1.fq C1_R1_2.fq

    Error:

    [Tue Mar 27 17:12:31 2012] Processing bowtie hits
    Traceback (most recent call last):
    File "/home/bitl/software/bin/tophat", line 3063, in <module>
    sys.exit(main())
    File "/home/bitl/software/bin/tophat", line 3029, in main
    user_supplied_deletions)
    File "/home/bitl/software/bin/tophat", line 2646, in spliced_alignment
    right_reads_map = maps[1].unspliced_bwt
    AttributeError: 'list' object has no attribute 'unspliced_bwt'

    I am using Ubuntu 11.10, 64 bit.

    Is it because of RAM? cause mine is only 4GB. I ordered 16GB RAM, expecting soon.

    Thank you for your time ^^

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