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assignments:ex9 [2018/10/11 13:19]
dokuroot
assignments:ex9 [2018/10/11 13:20] (current)
dokuroot
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 **c.** Make a new directory name '​ecoli_bowtie'​ and change into it. \\ \\ **c.** Make a new directory name '​ecoli_bowtie'​ and change into it. \\ \\
 **d.** Build a bowtie index: **d.** Build a bowtie index:
-  $ bowtie2-build -number_of_threads path_to_ecoli.fa ecoli+  $ bowtie2-build -number_of_threads path_to_ecoli.fa ecoli
 **2.** Change into the directory containing the fastq files '/​Users/​bz360/​Desktop/​e_coli_xbowtie_data'​ and run bowtie2 to map reads using the fastq files in the folder and the bowtie index from step 1 (run time ~15 min): **2.** Change into the directory containing the fastq files '/​Users/​bz360/​Desktop/​e_coli_xbowtie_data'​ and run bowtie2 to map reads using the fastq files in the folder and the bowtie index from step 1 (run time ~15 min):
-  $ bowtie2 -number_of_threads -x path_to_index/​prefix_of_index -1 fastq_file_mate1 -2 fastq_file_mate1 ​ -S output_file.sam+  $ bowtie2 -number_of_threads -x path_to_index/​prefix_of_index -1 fastq_file_mate1 -2 fastq_file_mate1 ​ -S output_file.sam
 * Record the number of reads that mapped in your lab notebook. \\ \\ * Record the number of reads that mapped in your lab notebook. \\ \\
 **3.** Use samtools (http://​samtools.sourceforge.net) to convert the sam formatted file to binary bam format: **3.** Use samtools (http://​samtools.sourceforge.net) to convert the sam formatted file to binary bam format:
assignments/ex9.txt ยท Last modified: 2018/10/11 13:20 by dokuroot