01 May Midterm Exam1. Collect DNA sequences
Midterm Exam
1. Collect DNA sequences
a. From the previous assignment collect all genomic.fna files from reference genomes.
i. Make sure all are extracted from their .gz format; use gunzip –k (filename)
ii. Place all reference genomes into a folder called, “Genomic” and place that in ~/jhu/project/samples
iii. 1 million bp metagenome, A read is considered recruited if it is aligned to a reference with =30 bp and =80% identity.
2. Use of the FR-HIT
a. Please download FR-HIT from the following website:
i. http://weizhong-lab.ucsd.edu/frhit/download.php
ii. Download the linux pre-complied binary version to get (fr-hit-v0.7-x86_64.tar.gz)
b. If FR-HIT needs to be unzipped from tar.gz, then use the following command:
i. tar xvf file.tar.gz
c. The to run FR-HIT, type:
./fr-hit -a sample_genome.fa -d reference_genome.fa -c 90 -m 40 -w 120 -r 0 -o out.sop
-a is the sample file in FASTA format to test
-d is the reference file in FASTA format to align the sample file
-c is the threshold identity which in this case we are using >90%
-m is for the minimal alignment coverage for each read, which is 30 at default
-w minimal read length to use 2bp k-mer index step to 454 long reads, in this case 120
-r is how to report alignment hits, 0 means all
-o is the output file name and location if need be.
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