GitHub - megancamilla/Scripts-Work-Mac

Name	Name	Last commit message	Last commit date
Latest commit History 4 Commits
.DS_Store	.DS_Store
96well.py	96well.py
AccessMySQL.py	AccessMySQL.py
BLASTconservedgenes.sh	BLASTconservedgenes.sh
BLASTparse_tomakedenovoGFF.py	BLASTparse_tomakedenovoGFF.py
BLASTparse_tomakedenovoGFFJames.py	BLASTparse_tomakedenovoGFFJames.py
BLASTparse_tomakedenovoGFF_gdu.py	BLASTparse_tomakedenovoGFF_gdu.py
BLASTtoGFF_50percent.py	BLASTtoGFF_50percent.py
BWASW_denovomap.sh	BWASW_denovomap.sh
BWA_mapdenovo_to_ref_strict.sh	BWA_mapdenovo_to_ref_strict.sh
BWA_mapdenovo_to_ref_strict_spades.sh	BWA_mapdenovo_to_ref_strict_spades.sh
BamSAMtofasta.sh	BamSAMtofasta.sh
BedtoBlastcmd_fasta_form.py	BedtoBlastcmd_fasta_form.py
BlastX_remote.sh	BlastX_remote.sh
Blastn_shell_taboutput.sh	Blastn_shell_taboutput.sh
BowtietoIGV.sh	BowtietoIGV.sh
CalcN50_gnx.txt	CalcN50_gnx.txt
CompositionCalc.py	CompositionCalc.py
CountLociGATK.java	CountLociGATK.java
CountReadsGATK.java	CountReadsGATK.java
CysteineRichCalc.py	CysteineRichCalc.py
DNAcalc.sh	DNAcalc.sh
Delly_formatingloop.sh	Delly_formatingloop.sh
Delly_to_BED6script.py	Delly_to_BED6script.py
Denovo_qualityCHECK.sh	Denovo_qualityCHECK.sh
Denovo_qualityCHECK_scaffold.sh	Denovo_qualityCHECK_scaffold.sh
FastaFilesplitter.py	FastaFilesplitter.py
Fasta_completegenes.py	Fasta_completegenes.py
FastatoGff_forVero.py	FastatoGff_forVero.py
GATK3-30pipline.sh	GATK3-30pipline.sh
GATKBWA.sh	GATKBWA.sh
GATK_Realigner.sh	GATK_Realigner.sh
GATK_SelectVariants.sh	GATK_SelectVariants.sh
GATK_UnifiedGenotyper_mac.sh	GATK_UnifiedGenotyper_mac.sh
GATK_VQSR_recalibratih	GATK_VQSR_recalibratih
GATK_VQSR_recalibration.sh	GATK_VQSR_recalibration.sh
GATK_VQSR_recalibration2-7.sh	GATK_VQSR_recalibration2-7.sh
GATK_getFasta.sh	GATK_getFasta.sh
GATK_parse_INS_DEL_SNPS.py	GATK_parse_INS_DEL_SNPS.py
Get_SSCP.py	Get_SSCP.py
Get_Sprotein_mysql.py	Get_Sprotein_mysql.py
Get_UTR_script.py	Get_UTR_script.py
Get_expression_profile.py	Get_expression_profile.py
Get_fasta_for_GofI.py	Get_fasta_for_GofI.py
Get_fasta_for_GofI_KHK.py	Get_fasta_for_GofI_KHK.py
Grab_secretedProteins.sh	Grab_secretedProteins.sh
James_GATK.sh	James_GATK.sh
Jamesmakeintervals.sh	Jamesmakeintervals.sh
Lastz_alignment.sh	Lastz_alignment.sh
Lastz_anyornone.sh	Lastz_anyornone.sh
MakeBlastdatapase.sh	MakeBlastdatapase.sh
ManipulatingLists.py	ManipulatingLists.py
Meme_submit.sh	Meme_submit.sh
Mgram_gff_gff3 2.sh	Mgram_gff_gff3 2.sh
Mgram_gff_gff3.sh	Mgram_gff_gff3.sh
Multi_isolate_fasta_maker.sh	Multi_isolate_fasta_maker.sh
MySQL_proteinlength.py	MySQL_proteinlength.py
My_SQL_directinput.txt	My_SQL_directinput.txt
Percent_Genes_Missing_CoreAcc.R	Percent_Genes_Missing_CoreAcc.R
Plotting_chromosomes_Genome_Fig_XX.R	Plotting_chromosomes_Genome_Fig_XX.R
Plotting_exondeletions_accross_chromosome.R	Plotting_exondeletions_accross_chromosome.R
Pycogent_Import_fasta.sh	Pycogent_Import_fasta.sh
PythonBLast_SearchIOparser.py	PythonBLast_SearchIOparser.py
PythonBlast_SearchIOparser.py_beta.sh	PythonBlast_SearchIOparser.py_beta.sh
PythonUserInput.sh	PythonUserInput.sh
Python_NCBI_BLAST.py	Python_NCBI_BLAST.py
README.md	README.md
RIP_GATK_pipeline.sh	RIP_GATK_pipeline.sh
RIPvariants_script.txt	RIPvariants_script.txt
RIPvcf_Non-synon_only_oneIsolate.sh	RIPvcf_Non-synon_only_oneIsolate.sh
RIPvcf_genesonly_oneIsolate.sh	RIPvcf_genesonly_oneIsolate.sh
RIPvcf_oneIsolate.sh	RIPvcf_oneIsolate.sh
Range_reverse.py	Range_reverse.py
Rcode_coverageplots	Rcode_coverageplots
ReadingandWriting.sh	ReadingandWriting.sh
RevComplement.py	RevComplement.py
SAMtoBAM.sh	SAMtoBAM.sh
SNP_EFF_parsetotabdelim.txt	SNP_EFF_parsetotabdelim.txt
SNPeff_tabedelim_filterer.py	SNPeff_tabedelim_filterer.py
SamBCFVariantCalling.sh	SamBCFVariantCalling.sh
SamtoFastq.sh	SamtoFastq.sh
Scaffolding_SSPACE.sh	Scaffolding_SSPACE.sh
SearchSnToxfiles_RegExp.sh	SearchSnToxfiles_RegExp.sh
Sort_Mapped_UN_Mappedreads_GATK.sh	Sort_Mapped_UN_Mappedreads_GATK.sh
Startcodon_secreted.fas	Startcodon_secreted.fas
Startcodonfinder.py	Startcodonfinder.py
TrackACgenes.py	TrackACgenes.py
Tritici_samtobam.sh	Tritici_samtobam.sh
UTR_and_Range_reverse.py	UTR_and_Range_reverse.py
UnifiedGenotyper.sh	UnifiedGenotyper.sh
Userinput.py	Userinput.py
VCF_filterer.py	VCF_filterer.py
VCF_get_SSP.py	VCF_get_SSP.py
VCF_get_SSP_foreli.py	VCF_get_SSP_foreli.py
VCF_parse_bashcut.txt	VCF_parse_bashcut.txt
ZeroCov_regionsBed.py	ZeroCov_regionsBed.py
Ztritici_createdatabase.sql	Ztritici_createdatabase.sql
Ztritici_nucmer.sh	Ztritici_nucmer.sh
align2ref.sh	align2ref.sh
align2refcdna.sh	align2refcdna.sh

Name

Last commit message

Last commit date

BLASTconservedgenes.sh

BLASTparse_tomakedenovoGFF.py

BLASTparse_tomakedenovoGFFJames.py

BLASTparse_tomakedenovoGFF_gdu.py

BLASTtoGFF_50percent.py