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SNPs
andrii
bisulfite
dynGenomClass
emptySites
findPackMule
find_mping_insertions
gff_and_seqfeaturestore_scripts
maize
mini_assemblies_and_bp_freq
pong
process_raw_paired_reads_2_split_by_target
process_reads
utilities
Q.pl
Q.pl~
Q.sh
Q_all.pl
Q_all.pl~
README
README_forBrowser
README_goodPingNames
RNAseq_graph.pl
SNP_tab_2_tableForGraph_RIL39_HEG4.pl
SmedASXL_018810
VelvetOptimiser.pl
add_good_ping_name_to_gff.pl
align_convert.pl
bam2pindel.pl
bam2pindel.pl-0.2.2
bowtie2sam.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_v2.pl
calculate_percent_methylation_per_gene_v2.pl~
calculate_range_percent_methylation.pl
calculate_range_percent_methylation.pl~
calculate_range_percent_methylation_for_primers.pl
cat_fq.pl
cat_fq_shell.pl
change_readgroup.pl
characterizer.pl
check_align_sh.pl
check_primers.pl
check_primers.pl~
check_primers_2013.pl
check_primers_Fall2012.pl
check_primers_Fall2012.pl.blastout
check_primers_Fall2012.pl.fa
check_primers_Fall2012.pl~
check_primers_Fall2012_2primers.pl
check_primers_Fall2012_2primers.pl~
check_raw_log.sh
check_sh.e_files.sh
cleanFasta.pl
cleanFasta.pl~
clean_fasta.pl
clean_fasta.pl~
clean_pairs.pl
clean_pairs.pl~
clean_pairs_indexed.pl
clean_pairs_memory.pl
clean_up_after_process_reads.sh
combine_TE_gff.pl
combine_TE_gff.pl~
combine_data.pl
combine_empty_found.pl
combine_insert_gffs.pl
combine_insertsNearGenes_geneMethylation.pl
compare_relocate_between_libraries.pl
compare_strains.pl
compare_strains.pl~
compare_strains_in_vcf.pl
compare_strains_in_vcf.pl~
compare_strains_in_vcf_old_but_useful.pl
compare_strains_in_vcf_print_private.pl
compare_strains_in_vcf_print_private.pl~
construcTE.pl
construcTEr.pl
construcTEr.pl~
convert_bismark_sam_2_gff.pl
convert_bismark_sam_2_wig.pl
convert_extracted_methylation_2_gff.pl
convert_extracted_methylation_2_region_wig.pl
convert_extracted_methylation_2_region_wigsqlite.pl
convert_extracted_methylation_2_region_wigtie.pl
convert_extracted_methylation_2_wig.pl
convert_extracted_methylation_2_wig_noFasta.pl
convert_seqIO.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_compare_output.pl
count_every_base_in_bam_compare_output.pl~
create_any_complete_site_with_flanking.pl
create_data_for_browser_upload.pl
delete_qsub_stat_files.sh
delete_qsub_stat_files.sh~
dna2longest_orfFasta.pl
do_filtering.pl
do_filtering.pl~
do_filtering_v2.pl
excision_report.pl
excision_report.pl~
extract_coverage_from_range_in_bismark_sam.pl
fasta_2_gff.pl
fasta_2_gff.pl~
fasta_length.pl
fasta_length.pl~
fastq_clean_pairs.pl
fastq_clean_pairs.pl~
fastq_split.pl
filter_only.pl
findPackmule.pl
find_TE_in_reads_blat_parser.pl
find_TE_in_reads_blat_parser.pl~
find_TE_insertionSites.old
find_TE_insertionSites.pl
find_TE_insertionSites_bowtieSingles.pl
find_coordinate.pl
find_good_hits_to_ping.pl
find_inserts_near_genes.sh
find_loc.pl
find_mping_insertionSites.pl
find_mping_seqs.pl
find_nearby_genes.pl
find_uniq.pl
find_uniq_10.10.of.40.pl
fq2fa.pl
gatk_quality_score_recalibration.pl
gatk_realign.pl
gatk_realign.pl~
gatk_realign_merged.pl
gatk_realign_merged.pl~
gatk_realign_merged_recalibrate.pl
gatk_realign_merged_recalibrate.pl~
gbrowseCustom2gff3.pl~
gbrowseCustomInsert2gff3.pl
gbrowseCustomInsert2gff3.pl~
gbrowseCustomPrimerTrack.txt
gbrowseCustomPrimerTrack.txt~
gbrowseCustomPriner2gff3.pl
getMatefile.pl
getOptsLong.tmp
getOptsLong.tmpl.pl
getOptsLong.tmpl.pl~
getPrimers.sh
get_TE_insertion_site.pl
get_fa_of_te_trimmed_te_matching_reads.pl
get_features_bp_count.pl
get_fq_of_mpingTrimmed_mpingMatching_reads.pl
get_fq_of_mpingTrimmed_mpingMatching_reads_index.pl
get_fq_of_te_trimmed_te_matching_reads.pl
get_full_range.pl
get_go_for_insertions.pl
get_go_for_insertions.pl~
get_insert_size.sh
get_insert_size.sh~
get_insertions.bakup
get_insertions.pl
get_insertions.pl~
get_insertions_class.pl
get_insertions_class.pl~
get_intergenic.pl
get_intergenic_with_array.pl
get_intron.pl
get_methylation_on_primers.pl
get_methylation_on_primers_faster.pl
get_mping_fa_from_each_read.pl
get_mping_insertion_site.pl
get_nt_freq_at_each_pos.pl
get_seq_from_table.pl
get_subseq_from_postition.pl
get_subseq_from_postition_BATCH.pl
get_subseq_from_postition_BATCH.pl~
get_subseq_from_range.pl
get_subseq_from_range_plusPadding.pl
get_subseq_from_range_plusPadding.pl~
get_subseqs_25flank_25TE.pl
get_subseqs_complete_TE.pl
get_subseqs_emptySites_TE.pl
get_subseqs_for_PCR.pl
get_subseqs_for_PCR.pl~
get_te_flanking_reads.pl
get_uniqMappedReads.pl
index_fq.pl
makeEmptySites.pl
makeEmptySites.pl~
makeEmptySites_mPing_with_flank.pl
makeEmptySites_mPing_with_flank.pl~
makeInsertBinary4Tree.pl
makeInsertBinary4Tree.pl~
makePrimers.pl
makeSeqForTree.pl
makeTable.pl
makeTableForGraph.pl
make_454_sam2fq_sh.pl
make_GATK_recalibrate.pl
make_SNP_makefile.pl
make_SNP_makefile.pl~
make_SNPs.pl
make_SNPs.pl~
make_SNPs_VQSR.pl
make_SNPs_VQSR.pl~
make_align_sam.pl
make_assemblies_from_insertion_fq_list.pl
make_assemblies_from_insertion_fq_list_for_each.pl
make_assemblies_from_insertion_fq_list_for_each.pl~
make_assemblies_from_te_containing_reads.pl
make_cat_fq_by_target_and_pair.pl
make_combineFQ_perLibrary.pl
make_config_file.pl~
make_extract_convert.sh
make_fake_methylated_seqs.pl
make_fastq2fasta_sh.pl
make_fq2fa.pl
make_genotype_makefile.pl
make_genotype_makefile.pl~
make_genotype_makefile_cornell.pl
make_genotype_makefile_cornell.pl~
make_makefile.pl~
make_mping_ref_gff.pl
make_primers.pl
make_primers.pl~
make_runBismark.sh
make_sam2fq_tmpDir.pl
make_trim_align_pair_sh.pl
make_trim_align_pair_tmp_dir_sh.pl
merge_bam.pl
merge_bam_and_create_merged_sam.pl
merge_bam_and_create_merged_sam_shell.pl
move_files.pl
mping_homozygous_heterozygous.pl
obsolete_cleanUpPairs_fq.pl
orientate_seqs.pl
parseBlast_mule.pl
parseBlast_packmule_inserts.pl
parsePindelOutFiles.pl
parsePrimer3.pl
parse_blatout.pl
parse_blatout_empty_site.pl
parse_blatout_empty_site.pl~
parse_blatout_empty_sites.pl
parse_blatout_sites.pl
parse_glsearch8c.pl
parse_glsearch8c.pl~
peaks.pl
perltidy
pindel
process_raw_reads_qsub.pl
process_raw_reads_qsub.pl~
process_reads_SNPs.pl
process_reads_SNPs.pl~
process_reads_SNPs.sh
process_reads_SNPs.sh~
process_reads_VQSR.sh
process_reads_VQSR.sh~
process_reads_genotype.sh
process_reads_genotype.sh~
process_reads_jason.sh~
query_seqFeatureStore_and_bam.pl
random_insertions.pl
raw_paired_reads_2_split_by_target.pl
reformat_maize_genome.pl
reformat_relocate_2_gff.pl
relocaTE.pl
relocaTE_align.pl
relocaTE_fq2fa.pl
relocaTE_insertionFinder.pl
relocaTE_prep.pl
relocaTE_process.pl
relocaTE_trim.pl
removeHets.pl
remove_duplicate_reads.pl
rename_files.pl
rename_files.pl_old_but_works
rename_files.pl~
rename_files_cornell.pl
rename_files_cornell.pl~
rename_files_cornell.pl~~
rename_fq.pl
run_blat.pl
run_combine.sh
run_construcTEr.pl
sam2bam.pl
sam2bam_scratch.pl
sam2fq.pl
sam2fq.pl_org
splitOnNNNNN.pl
splitPairs.pl
splitSam_byTarget.pl
splitSam_byTarget_tmpDir.pl
split_fasta.pl
split_fasta.pl~
split_fasta~
split_methyl_many_files.pl
split_methyl_many_files_noFasta.pl
submit_array_jobs.pl
sync_commit.log
sync_commit.sh
sync_commit.sh~
sync_push.log
sync_push.sh
test_fastq_id_parser.pl
threeAgree.pl
throwOutRepeatRegionSNPs.pl
throwOutRepeatRegionSNPs.sh
throwOutRepeatRegionSNPs.sh~
uniqSeqOnly4fq.pl
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