>
> dear Martin:
>          your answer is quite clear. i will try  Biostrings::matchPDict to
> map the reads of each sample to the assembled transcriptome using those
> samples.
>
>          but what i worrry is the efficiency. i can also use BWA OR bowtie
> to do so.
>
> i donot know if Biostrings::matchPDict  will be very slow?
>
> thank you
>
> shan gao
>

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