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  • how to perform mapping if refrence is small

    Hello,
    i have a sequence of a gene of my interest which is 700 bp long . I want to align my processed illumina data with this sequence of a gene ( taking it as a reference sequence). I used tohat program for this but it give error during splice junction formation.but it runs by bowtie. by using bowtie mapping file (.sam) i have run cuffling program and another program like htseq for read count. but i am unable to count reads.please tell me if anyone have any idea about how to aling reads if refrence is small.

  • #2
    Using a totally not-related-to-your-topic thread to ask a question is not likely to get much of a response. I suggest starting a new topic with your question and put in more detail than "unable". That said, mapping with bowtie2 and then looking at the resultant SAM/BAM file will give you read counts. htseq should also give you the counts although its method is a bit complex for just one gene.

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    • #3
      moved to new thread...

      ppant, post new questions in new threads...thanks.

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      • #4
        Reference you want to use may be small but do the reads in your sample derive from a larger genome?

        You could easily use an alternate aligner like Rick suggested (BBMap would be simple to use) (or even blat/blast) to align only against the smaller reference but the aligner may end up aligning some reads may actually be from a different part of the genome. If this 700 bp reference is contiguous you could consider the number of reads that successfully align as your count.
        Last edited by GenoMax; 07-01-2014, 06:58 AM.

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