Reference sequence reference whole genome contig

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Unformatted text preview: ile Resequencing RNA Seq SNPs Understanding the Input and Output of BWA Sequence Alignment/Map Format Sequence Reads + Reads: Illumina or 454 reads. Reference Sequence Reference: whole genome, contig, chromosome. Alignment So9ware Most of the analysis happens when considering the SAM files. Resequencing BWA, Bowtie, mrsFAST, GSNAP. SAM File RNA Seq SNPs SAM format “A tab ­delimited text format consis0ng of a header sec0on, which is op0onal, and an alignment sec0on” Example Headers: @HD @SQ @SQ @SQ @RG VN:1.0 SO:coordinate SN:1 LN:249250621 AS:NCBI37 UR:file:/data/local/ref/GATK/human_g1k_v37.fasta M5:1b22b98cdeb4a9304cb5d48026a85128 SN:2 LN:243199373 AS:NCBI37 UR:file:/data/local/ref/GATK/human_g1k_v37.fasta M5:a0d9851da00400dec1098a9255ac712e SN:3 LN:198022430 AS:NCBI37 UR:file:/data/local/ref/GATK/human_g1k_v37.fasta M5:fdfd811849cc2fadebc929bb925902e5 ID:UM0098:1 PL:...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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