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  • LSC
    started a topic 08-07-2013: Big changes in LSC 0.3

    08-07-2013: Big changes in LSC 0.3

    08-07-2013: Big changes in LSC 0.3

    Many users met problems in downstream analyses by using the LSC output, because some output reads are only slightly-corrected, while others are well-corrected . In LSC 0.3, you have FASTQ output and also have correction score (SR length coverage percentage) to select the well-corrected reads for downstream analyses.

    In LSC 0.3, we have a few updates. They are very IMPORTANT updates, new features and small fixes

    Very IMPORTANT updates:

    Support for Bowtie2 and RazerS3 as initial aligners. Now, BWA, Bowtie2, RazerS3 and Novoalign work in LSC. Please see the comparison details of aligners in the "Short read - Long read aligner#manual".
    Added SR length coverage percentage on LR (SR-covered length/full length of corrected LR) to corrected_LR output file. Here is an example, where the last number 0.82 is the SR length coverage percentage on LR:
    >m111006_202713_42141_c100202382555500000315044810141104_s1_p0/18941/365_1361|0.82
    Added support for three modes for step-wise runs:
    mode 0: end-to-end
    mode 1: generating LR_SR.map file
    mode 2: correction step
    Generating FASTQ output format based on correction probability given short read coverage. Please refer to LSC paper and manual page for more details. You can select well-corrected reads for downstream analyses by using the quality in FASTQ output or SR length coverage percentage above. Please the the filtering in the "Output#manual".

    New features

    Used the python path in the cfg file instead of default user/bin path
    Added option (-clean_up) to remove intermediate files or not (Note: important/useful ones will still be there in temp folder)
    Support for input fastq format for LR (long reads) and/or SR (short reads)
    Updated default BWA and novoalign commands options
    Printing out original LR names in the output file
    Support for printing out version number using -v/-version option

    Small bug fixed

    Fixed in removing XZ pattern printed out at the end of some uncorrected_LR sequences
    Fixed samParser bug (which was ignoring some valid alignments in BWA output)
    Last edited by LSC; 08-07-2013, 09:47 PM.

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