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 With that, we're ready to get started on the first exercise.



1: BWA – Yeast ChIP-seq

Overview ChIP-seq alignment workflow with BWA


Code Block
bwa mem hg19/hg19.fa fq/human_rnaseq.fastq.gz > human_rnaseq_mem.sam

Check the length of the SAM file you generated with wc -l. Since there is one alignment per line, there must be 586266 alignments (minus no more than 100 header lines), which is more than the number of sequences in the FASTQ file. This is bwa mem can report multiple alignment records for the same read, hopefully on either side of a splice junction. These alignments can still be tied together because they have the same read ID.