Convert NCBI feature file

python ExtractingFeature.py /Bioinformatics/Users/zfu/2015_Nadine_Strep/00.RawData/D39_Feature.txt /Bioinformatics/Users/zfu/2015_Nadine_Strep/00.RawData/D39_Feature.bed 'gi|116075884|gb|CP000410.1|'

python ExtractingFeature.py /Bioinformatics/Users/zfu/2015_Nadine_Strep/00.RawData/TIGR4_Feature.txt /Bioinformatics/Users/zfu/2015_Nadine_Strep/00.RawData/TIGR4_Feature.bed 'gi|193804931|gb|AE005672.3|'

python ExtractingFeature.py /Bioinformatics/Users/zfu/2015_Nadine_Strep/00.RawData/R6_Feature.txt /Bioinformatics/Users/zfu/2015_Nadine_Strep/00.RawData/R6_Feature.bed 'gi|15902044|ref|NC_003098.1|'

QC strep reads

/share/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /share/apps/FastQC/FastQC-0.11.2/Configuration/contaminants_LJI.txt --casava -o /Bioinformatics/Users/zfu/2015_Nadine_Strep/ -t 2 /Bioinformatics/Users/zfu/2015_Nadine_Strep/URF918-2/02.Mapping/URF918-2.unaligned.fastq.gz &

/share/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /share/apps/FastQC/FastQC-0.11.2/Configuration/contaminants_LJI.txt --casava -o /Bioinformatics/Users/zfu/2015_Nadine_Strep/ -t 2 /Bioinformatics/Users/zfu/2015_Nadine_Strep/URF918-2/02.Mapping/URF918-2.aligned.fastq &

/share/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /share/apps/FastQC/FastQC-0.11.2/Configuration/contaminants_LJI.txt --casava -o /Bioinformatics/Users/zfu/2015_Nadine_Strep/ -t 2 /Bioinformatics/Users/zfu/2015_Nadine_Strep/URF918-1/02.Mapping/URF918-1.unaligned.fastq.gz &

/share/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /share/apps/FastQC/FastQC-0.11.2/Configuration/contaminants_LJI.txt --casava -o /Bioinformatics/Users/zfu/2015_Nadine_Strep/ -t 2 /Bioinformatics/Users/zfu/2015_Nadine_Strep/URF918-1/02.Mapping/URF918-1.aligned.fastq &

/share/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /share/apps/FastQC/FastQC-0.11.2/Configuration/contaminants_LJI.txt --casava -o /Bioinformatics/Users/zfu/2015_Nadine_Strep/ -t 2 /Bioinformatics/Users/zfu/2015_Nadine_Strep/9-2/02.Mapping/9-2.unaligned.fastq.gz &

/share/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /share/apps/FastQC/FastQC-0.11.2/Configuration/contaminants_LJI.txt --casava -o /Bioinformatics/Users/zfu/2015_Nadine_Strep/ -t 2 /Bioinformatics/Users/zfu/2015_Nadine_Strep/9-2/02.Mapping/9-2.aligned.fastq &

/share/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /share/apps/FastQC/FastQC-0.11.2/Configuration/contaminants_LJI.txt --casava -o /Bioinformatics/Users/zfu/2015_Nadine_Strep/ -t 2 /Bioinformatics/Users/zfu/2015_Nadine_Strep/9-1/02.Mapping/9-1.unaligned.fastq.gz &

/share/apps/FastQC/FastQC-0.11.2/fastqc --contaminants /share/apps/FastQC/FastQC-0.11.2/Configuration/contaminants_LJI.txt --casava -o /Bioinformatics/Users/zfu/2015_Nadine_Strep/ -t 2 /Bioinformatics/Users/zfu/2015_Nadine_Strep/9-1/02.Mapping/9-1.aligned.fastq &

VCF UNIQ DECOMPOSITION

cd /Bioinformatics/Users/zfu/2015_Nadine_Strep

/Bioinformatics/Users/zfu/packages/vt/vt decompose ./9-1/03.Freebayes/9-1_sorted.vcf -o ./9-1/03.Freebayes/9-1.decomposed.vcf

/Bioinformatics/Users/zfu/packages/vt/vt normalize ./9-1/03.Freebayes/9-1.decomposed.vcf -r ./00.RawData/Strep.fasta | /Bioinformatics/Users/zfu/packages/vt/vt uniq - -o ./9-1/03.Freebayes/9-1.normalized_uniq.vcf

/Bioinformatics/Users/zfu/packages/vt/vt decompose_blocksub ./9-1/03.Freebayes/9-1.normalized_uniq.vcf -o ./9-1/03.Freebayes/9-1.decomposed_blocksub.vcf

 ***********************************************

/Bioinformatics/Users/zfu/packages/freebayes/bin/freebayes -F 0.01 -p 1 --fasta-reference /Bioinformatics/Users/zfu/2015_Stephanie_BAC/00.RawData/clone.fasta /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/04.Clone/2014_clone_sorted.bam > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/06.Freebayes/2014_clone_sorted.vcf

/Bioinformatics/Users/zfu/packages/vcflib/bin/vcffilter -f "QUAL > 20" /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/06.Freebayes/2014_clone_sorted.vcf > /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/06.Freebayes/2014_clone_filtered.vcf

cd /Bioinformatics/Users/zfu/2015_Stephanie_BAC/2014/src/

python generateConsensusData_Ori.py ../06.Freebayes/2014_clone_sorted.vcf ../../00.RawData/oneLine.fasta/clone_oneLine.fasta ../07.Consensus.Fasta/2014_clone_Consensus.fa ../07.Consensus.Fasta/2014_clone_noGap_Consensus.fa  ../06.Freebayes/2014_clone_snpInfo.tsv


python generateConsensusData_Freq.py ../06.Freebayes/2014_clone_filtered.vcf ../../00.RawData/oneLine.fasta/clone_oneLine.fasta ../07.Consensus.Fasta/2014_clone_Consensus.filtered.fa ../07.Consensus.Fasta/2014_clone_noGap_Consensus.filtered.fa  ../06.Freebayes/2014_clone_snpInfo.filtered.tsv ../06.Freebayes/2014_clone_snpInfo.filtered_Freq.vcf

merge many files and remove the first line.

find . -name "*.extension" | xargs -n 1 tail -n +2

BIIB and ARE and INTC

BIIB:

测试200均线以后迅速反弹，以后止损应该设置在20/50/200均线下方一点的地方。

INTC:

好消息出来以后买进，结果迅速下跌。

ARE:

好消息出来以后没有买进，结果迅速下跌。