20211021

Contents

1. 1. Working directories
2. 2. SIBA
3. 3. SARS-CoV-2 Download
4. 4. URL
5. 5. NCBI database download
6. 6. HSV-2 BWA with magicblast
7. 7. COVID-19 data US
   1. 7.1. Data from HHS

Working directories

# 
#######################################################################
# 
# not successful with the codes as below
# ETE3 installation in X1
/media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/ETE3/Installers/Miniconda-latest-Linux-x86_64.sh -b -p ~/anaconda_ete/
# 
export PATH=~/anaconda_ete/bin:$PATH;
conda install -c etetoolkit ete3 ete3_external_apps # with default updating
#################
# Check installation
ete3 version
ete3 build check
# magicblast install
axel https://ftp.ncbi.nlm.nih.gov/blast/executables/magicblast/1.6.0/ncbi-magicblast-1.6.0-src.tar.gz
# UGENE Pro installation
cd /media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/UGENE/Installer
axel https://github.com/ugeneunipro/ugene/releases/download/40.1/ugene-40.1-linux-x86-64.tar.gz

SIBA

OK /media/ht/ht_5T/Work/References/Tech/DNA_Amplification/SIBA/Ref/3_SIBA.pdf
cd /media/ht/ht_5T/Work/References/Tech/DNA_Amplification/SIBA/Ref
ug /media/ht/ht_5T/Work/References/Tech/DNA_Amplification/SIBA/Ref/3_Template.gb

SARS-CoV-2 Download

1. NCBI Virus
2. Select “Download” from “SARS-CoV-2 Data Hub”

URL

• Virus-Host Database

NCBI database download

• Using NCBI edirect to access data at NCBI | ComputationalGenomicsManual

einfo -email xxx@sdsu.edu -dbs | sort

HSV-2 BWA with magicblast

subl /media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20191025/README.md
# 
i=/media/ht/ht_5T/Work/Experiments/Primers/Primer_Design/20191025/README.md; subl ${i}

1. Index RefSeq
2. BWA with 10 sequences

• herpes simplex virus type 2 HSV-2 (taxid:10310)

cp /media/ht/ht_5T/Work/Projects/Herpesvirus_Project/DB/CG/NC_001798_HSV-2.fas /home/ht/Downloads/HSV-2/
grep -o 'N' HSV-2_Test.fas | wc -l # includes lots of N nt, in total 44470
# 
###########################################################
# Index
# file:///media/ht/ht_5T/Bioinformatics/Bioinfo-Softs/NCBI/magicblast/magicblast_Learning.html#37_Align_FASTA_with_subject_sequence_instead_of_indexed_database
# 
cd ~/Downloads/HSV-2/DB
Input=NC_001798_HSV-2.fas
DatabaseName=HSV-2
makeblastdb -in ${Input} -dbtype nucl -parse_seqids -out ${DatabaseName}
# 
Ref=~/Downloads/HSV-2/DB/HSV-2
Seq=HSV-2_Test.fas
Seq_Base=`basename ${Seq}`; Ref_Base=`basename ${Ref%.*}`; BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`.bam
time magicblast -query ${Seq} -db ${Ref} -infmt fasta -outfmt sam | samtools view -bS -F 4 -> ${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam # 序列中绝对禁止`-`，这类符号是经过MSA产生的
# 
Ref=~/Downloads/HSV-2/DB/NC_001798_HSV-2.fas
Seq=HSV-2_Test.fas
Seq_Base=`basename ${Seq}`; Ref_Base=`basename ${Ref%.*}`; BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`.bam
time magicblast -query ${Seq} -subject ${Ref} -infmt fasta -outfmt sam | samtools view -bS -F 4 -> ${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam # 序列中绝对禁止`-`，这类符号是经过MSA产生的

real    0m3.335s
user    0m1.295s
sys    0m0.661s

BAM=${Seq_Base%.*}_vs_`basename ${Ref_Base}`_Mapped.bam
time samtools sort $BAM > "${BAM%.bam}.sort.bam"
time samtools index "${BAM%.bam}.sort.bam"
# 
Ref=
Tablet "${BAM%.bam}.sort.bam"

COVID-19 data US

Data from HHS

• Results matching topic of hhs covid-19 | Page 1 of 2 | HealthData.gov

赏

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