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IGV tools

IGV tools. Pipeline. Download genome from Ensembl bacteria database. Map reads to genome by CLC. Export the mapping reads file (SAM). Using the mapping reads file to find SNP by CLC. View sequence on IGV. Export SNP file by EXCEL. Download genome from Ensembl bacteria database.

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IGV tools

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  1. IGV tools

  2. Pipeline Download genome from Ensembl bacteria database Map reads to genome by CLC Export the mapping reads file (SAM) Using the mapping reads file to find SNP by CLC View sequence on IGV Export SNP file by EXCEL

  3. Download genome from Ensembl bacteria database Map reads to genome by CLC Export the mapping reads file (SAM) Using the mapping reads file to find SNP by CLC Export SNP file by EXCEL View sequence on IGV

  4. Download genome from Ensembl bacteria database Map reads to genome by CLC Export SNP file by EXCEL Export the mapping reads file (SAM) Using the mapping reads file to find SNP by CLC Download Excel file : http://163.25.92.70/class Export SNP file by EXCEL View sequence on IGV

  5. Using samtools Download genome from Ensembl bacteria database Map reads to genome by CLC SAM convert to BAM file Sort the BAM file Output the sorted BAM file Export the mapping reads file (SAM) Using the mapping reads file to find SNP by CLC Output the index BAM file Index the BAM file View sequence on IGV Export SNP file by EXCEL

  6. Download SAM file : http://163.25.92.70/class SAM convert to BAM file samtools view –bS (SAM) –T (Reference) –o (BAM) ex : samtools view –bS demo1.sam –T SAmu50Ebl.fa –o demo1.bam Sort the BAM file samtools sort (BAM) (BAM.sorted) ex : samtools sort demo1.bam demo1.sorted Index the BAM file samtools index (BAM.sorted) ex : samtools index demo1.sorted

  7. Download genome from Ensembl bacteria database Map reads to genome by CLC Export the mapping reads file (SAM) Using the mapping reads file to find SNP by CLC Export SNP file by EXCEL View sequence on IGV

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