禽流感数据分析记录
-
bwa mem GCA_013339765.1_ASM1333976v1_genomic.fna.gz ../12-DNA_L2_1.fq ../12-DNA_L2_2.fq > 12.bwa.sam samtools view -F4 -bh 12.bwa.sam -o 12.bwa.bam samtools sort -n 12.bwa.bam -o 12.bwa.sorted.bam samtools fastq -1 12_removed_host_R1.fq -2 12_removed_host_R2.fq -0 /dev/null -s /dev/null -n 12.bwa.sorted.bam megahit -1 ../1-remove_hosts/12_removed_host_R1.fq -2 ../1-remove_hosts/12_removed_host_R2.fq -o 12_megahit -
spades --meta 在组装的时候报申请不到内存的错误 可能小服务器的内存不够 换megahit组装
-
gisaid里面竟然有一条禽流感数据是错误的字符 mafft直接报错了
achickenpolandhnmpagatattgaaagatgagtcttctaaccgaggtcgaaacgtacgttctctctatcgtcccgtc
aggccccctcaaagccgagatcgcacagagacttgaagatgtctttgcagggaagaacaccgatcttgaggctctcatgg
aatggctaaagacaagaccaatcctgtcacctctgactaaggggattttagggtttgtgttcacgctcaccgtgcccagt
gagcgaggactgcagcgtagacgctttgtccaaaatgctctaaatggaaatggagacccaaacaacatggacagggcagt
caaactgtacaggaaattgaagagagagataacattccatggggctaaagaaattgcactcagttactcaactggtgcac
ttgccagttgtatgggtatcatatacaacaggatggggacggtaaccacagaagtggcattgggcctagtgtgtgccacc
tgtgagcagattgctgattcacagcatcggtctcacagacagatagcaaccaccaccaacccactaatcagacatgaaaa
cagaatggtgctggccagtactacagctaaggctatggagcagatggctgggtcgagtgagcaggcagcggaagccatgg
aggttgctagtcaggctaggcagatggtgcaggcgatgaggaccattggaactcatcctagctccagtgccggtctgaga
gatgatctccttgaaaatttgcaggcctaccagaaacggatgggagtgcaactgcagcgattcaagtgatcctctcgtta
ttgccgcaagtatcattgggatcttgcacttgatattgtggattcttgatcgccttttcttcaaatgcgtttatcgtcgc
cttaaatacggtttgaaaagagggccttctacggaaggagtgcctgagtctatgagggaagagtatcggcaggaacagca
gaatgctgtggatgttgacgatgatcattttgtcaacatagagctggagtaaaaaacta -
-
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4731279/
Quantifying influenza virus diversity and transmission in humans