https://github.com/eggnogdb/eggnog-mapper/issues/81

https://www.biostars.org/p/354264/
The site chr1:724953 overlaps with another variant, skipping...
The site chr1:797380 overlaps with another variant, skipping...
The fasta sequence does not match the REF allele at chr1:1298836:
.vcf: [CAGAG]
.vcf: [CAG] <- (ALT)
.fa: [GAGAG]TTTTGTTCTTTTGCTCAGGATGGAGAGCAGTGGTGCAATC
在做consensus的时候 indel 会导致错误 我们只选择snp来做consensus

https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide&VirusLineage_ss=Wuhan seafood market pneumonia virus, taxid:2697049&utm_source=gquery&utm_medium=referral&utm_campaign=COVID-19
NCBI 病毒数据库

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7462517/
用了4个多序列比对软件 然后进行综合
9bb11eda-6c73-487c-91c5-ecc13ae901de-image.png

https://www.sciencedirect.com/science/article/pii/S1476927121001699#tbl0005
Comprehensive analyses of bioinformatics applications in the fight against COVID-19 pandemic
生信在抗击新冠过程中的作用，
bf3cad91-c1ac-4f19-ac31-0220b416adac-image.png
一，新冠常用的数据库
Table 1. Databases of genome and protein structure.

Type Data center
Genome sequence Global Initiative on Sharing Avian Influenza Data (GISAID, https://www.gisaid.org)
Genome sequence National Center for Biotechnology Information (NCBI, https://www.ncbi.nlm.nih.gov)
Genome sequence National Microbiology Data Center (NMDC, https://www.nmdc.cn)
Genome sequence China National GeneBank (CNGB, https://www.cngb.org)
Genome sequence China National Center for Bioinformation (CNCB, https://bigd.big.ac.cn/ncov)
Protein sequence/function Universal Protein (UniProt, https://www.uniprot.org)
Protein sequence/structure Research Collaboratory for Structural Bioinformatics Protein Data Bank Database (RCSB PDB, https://www.rcsb.org)
二，

程老师 6个样本

2. /opt/hisat2-2.1.0/extract_splice_sites.py /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf > /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX.ss /opt/hisat2-2.1.0/extract_exons.py /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf > /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX.exon /opt/hisat2-2.1.0/hisat2-build -p 8 --ss /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX.ss --exon /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX.exon /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/GCF_000001405.39_GRCh38.p13_genomic.fa chrX_tran docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H040_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H040_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C029_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C029_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H036_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H036_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C028_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C028_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H009_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/H009_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 hisat2 --dta -x /ceph_disk2/data/hongyuan/tmp/six_sample/my_index/chrX_tran -1 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C030_1.fq.gz -2 /ceph_disk2/data/hongyuan/mnt/data/find_data/BC180196-1/data/C030_2.fq.gz -S /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/aleksandar_danicic/bismark-0-21-0:0 samtools sort -o /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.bam /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.sam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.bam -l C028 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/C028.gtf docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.bam -l C029 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/C029.gtf docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.bam -l C030 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/C030.gtf docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.bam -l H009 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/H009.gtf docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.bam -l H036 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/H036.gtf docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.bam -l H040 -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/H040.gtf docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie --merge -p 8 -G /ceph_disk2/data/hongyuan/mnt/data/public_data/Ref/human/Homo_sapiens.GRCh38.105.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/mergelist.txt docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/C028/C028.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/C028.bam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/C029/C029.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/C029.bam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/C030/C030.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/C030.bam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/H009/H009.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/H009.bam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/H036/H036.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/H036.bam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 /opt/stringtie-1.3.3.Linux_x86_64/stringtie -e -B -p 8 -G /ceph_disk2/data/hongyuan/tmp/six_sample/assembly/stringtie_merged.gtf -o /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown/H040/H040.gtf /ceph_disk2/data/hongyuan/tmp/six_sample/map/H040.bam docker run -d -v /ceph_disk2/data/hongyuan:/ceph_disk2/data/hongyuan -v /ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu:/ceph_disk2/software/hisat/data/ftp.ccb.jhu.edu images.sbgenomics.com/marko_milanovic/stringtie:1.3.3 python /prepDE.py -i /ceph_disk2/data/hongyuan/tmp/six_sample/ballgown

https://learn.bybit.com/altcoins/what-is-genopets-gene-token/

使用ena的api查询srr的ftp地址
https://ena-docs.readthedocs.io/en/latest/retrieval/programmatic-access.html

POST /ena/portal/api/search HTTP/1.1 Host: www.ebi.ac.uk Content-Type: application/x-www-form-urlencoded Cache-Control: no-cache Postman-Token: 57478685-1ce1-7848-aaab-20538ea63a03 format=json&includeAccessions=ERR1726424&result=read_run&fields=all