Is it possible to estimate execution time for Bowtie2 ?
I have a reference that is 1Gb in size, and two sets of reads with the same size. How to estimate the execution time of Bowtie2 given the features of my machine?
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Ram
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Esther Brasil •
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Esther Brasil •
2 answers
Honestly, your best bet is to just align a million reads or so (see the -u option) and extrapolate from that.
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Devon Ryan
Approximately, yes.
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Devon Ryan
1. use `bowtie2-build` to build index for the reference: bowtie2-build reference**.fa a_custom_name_as_index_name
2. use bowtie to align reads to the reference geneme: bowtie2 -p thread_num -x a_custom_name_as_index_name -1 left_reads.fq -2 right_reads.fq -S output_alignment_results.sam
tophat/HAIST -> bowtie2
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