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  • contigs generation via gsnap -> cufflinks

    Two little questions:
    1) I mapped 454 rna-seq reads to their reference chromosomes using Gsnap. It worked smoothly but I didn't like to see that only 55%-60% of the reads were mapped. Are these percentages reasonable, based on your experience ?

    2) After feeding my gsnap sam/bam alignments into cufflinks, I eventually got what seems to be a large list of putative transcripts and splice variants mapped to the referece chromosomes (gtf files, *.fpkm_tracking).
    Now I need also to extract the transcript sequences themselfs (not just the exon positions) - is there a ready-made way to do that ?

    Many thanks

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