Download 22 Illumina library production, MITOBIM,MITOS

Method/name
What it does
Extracts DNA,
Removes RNA,
QC
output
fastQC
Trimmomatic
MitoBIM
MITOS
Removes failed seq
From BAIT/SEED extends
Annotates gene content
comments
genomic DNA ≥ 20kbp, RNA-free,
OK A230/260/280 values
Adequate amount
CTAB extraction,gel,spec
Galaxy, Bioinformatics
Use previously recorded sequence, like CO1,
16S or full mitochondria of related
organisms, to computationally reconstruct
from 150bp PE Illumina reads the
mitochondrial genome sequence from the
samples analyzed
Handout 22 446/546L 14 November
Log on to Galaxy:
http://emil.unm.edu:8080
login email without @unm.edu
pw localgalaxy
go to shared data
select AdemaClass2016
select fastq and reference, import into history (name history)
go to analyze data
left pane NGS: QC and manipulations
interleave
2,4,5,8 select ph2.read1.fastq and ph2.read1.fastq
1,3,6, select ech.read1.fastq and ech.read1.fastq
7,9,10 select hel.read1.fastq and hel.read1.fastq
execute
for resulting file:
left pane NGS mapping
Mitobim
Select baiting:
2,4,5,8 ref_mt_Ph2.fasta
1,3,6, ref_mt_Ech.fasta
7,9,10 ref_mt_Bg.fasta
for readpool in fastqformat: select interleave result
Set iterations to 150
Execute
Send resulting fasta file
to http://mitos.bioinf.uni-leipzig.de/index.py
Use correct genetic code
AND
To BLASTN (Not mega blast) NCBI versus gastropoda (Ph2 or Hel)
Or strigeidea (Ech)