2021-11-19 短序列手动组装

cd /home/andy/data/other_project/xjf/

#fastq convert to fasta:
cat /home/public/sequence_datas/01_zhy_genome/clean_data/cixingtou3DNA1-26_HL3FTCCXY_L1_2.clean.fq  | paste - - - - | sed 's/^@/>/g'| cut -f1-2 | tr '\t' '\n' > female1.2.fasta

#make blast database
makeblastdb -dbtype nucl -in female1.2.fasta -out female1.2.fasta_db


#blastn short
blastn -query miRNA -db /home/andy/data/other_project/xjf/database/female1.2.fasta_db -out female_1.2_genome_miR275 -evalue 100 -task blastn-short


#extract target sequence
source activate python2
cd /home/andy/data/other_project/xjf/extract/
filter_fasta.py -f /home/andy/data/other_project/xjf/female1.2.fasta -o /home/andy/data/other_project/xjf/extract/01_miR275_genome -s /home/andy/data/other_project/xjf/extract/list_1


#assemble the candidate sequence using Trinity
source activate RNAseq
cd /home/andy/data/other_project/xjf/trinity_assemble/
Trinity --seqType fa --single /home/andy/data/other_project/xjf/extract/01_miR275_genome --CPU 20 --max_memory 50G --output 01_trinity_miRNA275_genome --min_contig_length 120 

Trinity --seqType fa --single /home/andy/data/other_project/xjf/extract/02_miR275_genome --CPU 20 --max_memory 50G --output 02_trinity_assemble/Trinity_miRNA275_genome --min_contig_length 100