GitHub - srobb1/scripts_by_sofia: my scripts

Branches Tags

Name		Name	Last commit message	Last commit date
Latest commit History 149 Commits
SNPs		SNPs
andrii		andrii
bisulfite		bisulfite
dynGenomClass		dynGenomClass
emptySites		emptySites
findPackMule		findPackMule
find_mping_insertions		find_mping_insertions
gff_and_seqfeaturestore_scripts		gff_and_seqfeaturestore_scripts
maize		maize
mini_assemblies_and_bp_freq		mini_assemblies_and_bp_freq
pong		pong
process_raw_paired_reads_2_split_by_target		process_raw_paired_reads_2_split_by_target
process_reads		process_reads
utilities		utilities
Q.pl		Q.pl
Q.pl~		Q.pl~
Q.sh		Q.sh
Q_all.pl		Q_all.pl
Q_all.pl~		Q_all.pl~
README		README
README_forBrowser		README_forBrowser
README_goodPingNames		README_goodPingNames
RNAseq_graph.pl		RNAseq_graph.pl
SNP_tab_2_tableForGraph_RIL39_HEG4.pl		SNP_tab_2_tableForGraph_RIL39_HEG4.pl
SmedASXL_018810		SmedASXL_018810
VelvetOptimiser.pl		VelvetOptimiser.pl
add_good_ping_name_to_gff.pl		add_good_ping_name_to_gff.pl
align_convert.pl		align_convert.pl
bam2pindel.pl		bam2pindel.pl
bam2pindel.pl-0.2.2		bam2pindel.pl-0.2.2
bowtie2sam.pl		bowtie2sam.pl
calculate_percent_methylation.pl		calculate_percent_methylation.pl
calculate_percent_methylation.pl~		calculate_percent_methylation.pl~
calculate_percent_methylation_per_gene.pl		calculate_percent_methylation_per_gene.pl
calculate_percent_methylation_per_gene.pl~		calculate_percent_methylation_per_gene.pl~
calculate_percent_methylation_per_gene_v2.pl		calculate_percent_methylation_per_gene_v2.pl
calculate_percent_methylation_per_gene_v2.pl~		calculate_percent_methylation_per_gene_v2.pl~
calculate_range_percent_methylation.pl		calculate_range_percent_methylation.pl
calculate_range_percent_methylation.pl~		calculate_range_percent_methylation.pl~
calculate_range_percent_methylation_for_primers.pl		calculate_range_percent_methylation_for_primers.pl
cat_fq.pl		cat_fq.pl
cat_fq_shell.pl		cat_fq_shell.pl
change_readgroup.pl		change_readgroup.pl
characterizer.pl		characterizer.pl
check_align_sh.pl		check_align_sh.pl
check_primers.pl		check_primers.pl
check_primers.pl~		check_primers.pl~
check_primers_2013.pl		check_primers_2013.pl
check_primers_Fall2012.pl		check_primers_Fall2012.pl
check_primers_Fall2012.pl.blastout		check_primers_Fall2012.pl.blastout
check_primers_Fall2012.pl.fa		check_primers_Fall2012.pl.fa
check_primers_Fall2012.pl~		check_primers_Fall2012.pl~
check_primers_Fall2012_2primers.pl		check_primers_Fall2012_2primers.pl
check_primers_Fall2012_2primers.pl~		check_primers_Fall2012_2primers.pl~
check_raw_log.sh		check_raw_log.sh
check_sh.e_files.sh		check_sh.e_files.sh
cleanFasta.pl		cleanFasta.pl
cleanFasta.pl~		cleanFasta.pl~
clean_fasta.pl		clean_fasta.pl
clean_fasta.pl~		clean_fasta.pl~
clean_pairs.pl		clean_pairs.pl
clean_pairs.pl~		clean_pairs.pl~
clean_pairs_indexed.pl		clean_pairs_indexed.pl
clean_pairs_memory.pl		clean_pairs_memory.pl
clean_up_after_process_reads.sh		clean_up_after_process_reads.sh
combine_TE_gff.pl		combine_TE_gff.pl
combine_TE_gff.pl~		combine_TE_gff.pl~
combine_data.pl		combine_data.pl
combine_empty_found.pl		combine_empty_found.pl
combine_insert_gffs.pl		combine_insert_gffs.pl
combine_insertsNearGenes_geneMethylation.pl		combine_insertsNearGenes_geneMethylation.pl
compare_relocate_between_libraries.pl		compare_relocate_between_libraries.pl
compare_strains.pl		compare_strains.pl
compare_strains.pl~		compare_strains.pl~
compare_strains_in_vcf.pl		compare_strains_in_vcf.pl
compare_strains_in_vcf.pl~		compare_strains_in_vcf.pl~
compare_strains_in_vcf_old_but_useful.pl		compare_strains_in_vcf_old_but_useful.pl
compare_strains_in_vcf_print_private.pl		compare_strains_in_vcf_print_private.pl
compare_strains_in_vcf_print_private.pl~		compare_strains_in_vcf_print_private.pl~
construcTE.pl		construcTE.pl
construcTEr.pl		construcTEr.pl
construcTEr.pl~		construcTEr.pl~
convert_bismark_sam_2_gff.pl		convert_bismark_sam_2_gff.pl
convert_bismark_sam_2_wig.pl		convert_bismark_sam_2_wig.pl
convert_extracted_methylation_2_gff.pl		convert_extracted_methylation_2_gff.pl
convert_extracted_methylation_2_region_wig.pl		convert_extracted_methylation_2_region_wig.pl
convert_extracted_methylation_2_region_wigsqlite.pl		convert_extracted_methylation_2_region_wigsqlite.pl
convert_extracted_methylation_2_region_wigtie.pl		convert_extracted_methylation_2_region_wigtie.pl
convert_extracted_methylation_2_wig.pl		convert_extracted_methylation_2_wig.pl
convert_extracted_methylation_2_wig_noFasta.pl		convert_extracted_methylation_2_wig_noFasta.pl
convert_seqIO.pl		convert_seqIO.pl
correct_ref_with_reseq.pl		correct_ref_with_reseq.pl
correct_ref_with_reseq.pl~		correct_ref_with_reseq.pl~
count_every_base_in_bam.pl		count_every_base_in_bam.pl
count_every_base_in_bam.pl~		count_every_base_in_bam.pl~
count_every_base_in_bam_compare_output.pl		count_every_base_in_bam_compare_output.pl
count_every_base_in_bam_compare_output.pl~		count_every_base_in_bam_compare_output.pl~
create_any_complete_site_with_flanking.pl		create_any_complete_site_with_flanking.pl
create_data_for_browser_upload.pl		create_data_for_browser_upload.pl
delete_qsub_stat_files.sh		delete_qsub_stat_files.sh