Notes on the NGS course

NGS_notes.ipnb

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      "Extensions of the file\n",
      "======================\n",
      "\n",
      "This is the content of the genome folder:\n",
      "\n",
      "```\n",
      "participant@hook-norton:~/Desktop/RNA-seq$ ls genome/\n",
      "Danio_rerio.Zv9.66.dna.fa      ZV9.1.ebwt  ZV9.4.ebwt\n",
      "Danio_rerio.Zv9.66.dna.fa.fai  ZV9.2.ebwt  ZV9.rev.1.ebwt\n",
      "zebrafish.zv9.genome           ZV9.3.ebwt  ZV9.rev.2.ebwt\n",
      "```\n",
      "Important extensions\n",
      "--------------------\n",
      "\n",
      "   \n",
      "    * .fa --> FASTA file \n",
      "    * .fai --> FASTA file indexed format\n",
      "    * .ebwt --> Indexed extension for the bowtie aligment `bowtie -m 1 -S bowtie_index.mm10 Oct4.fastq > Oct4.sam`\n",
      "      Bowtie aligns the reads to the genome, so you know which part of the genome has been transcribed.\n",
      "    * .bam --> Binary format created by SAmtools (Can be sorted or unsorted)\n",
      "    * .bai --> Index for the bam file\n",
      "\n",
      "\n"
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