how to perform mapping if refrence is small

[GenoMax]

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.

[ECO]

moved to new thread...

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

[westerman]

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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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.