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Bwa single end alignment

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I am trying to align Genomic DNA sequence reads 64 bases in length to reference human genome. The sequence reads are single ended. I am using bwa to align. I want to extract reads those are perfectly matches to reference genome.
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alignment - Difference between BWA-backtrack and BWA-MEM - Bioinformatics Stack Exchange

Bwa Index Output. But these brand-new SPACs have single-digit billion market caps and massive potential as. By default, the output from the extract command will be sent to standard output unless otherwise defined with the option -o. The triggering of the output conditions can be defined by the access sequences and routines associated with it.
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List of RNA-Seq bioinformatics tools

We are also going to use two different but popular mapping tools, bwa and bowtie. In the box that pops up, make sure to pick a specific availability zone for both the volume and the EC2 instance to be run in — e. Now go launch your AMI instance.
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The "time" command infront of the commands will time how much time was actually spent on the job. Note down the time for each command, it is the third number that is written, something like m:s. First go to your work dir, create a folder for the exercise and copy data to there I wrote down all the commands, but you probably know how to do you. Lets look at the header and the alignment of the alignment we made before -h tells samtools to also show the header. Header lines starts with " ", " SQ" are all the sequences you mapped against in your reference fasta file.
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