GitHub - 52teth/PacBio-generic: General (non-project specific) collection of scripts

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General (non-project specific) collection of scripts

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Name		Name	Last commit message	Last commit date
Latest commit History 48 Commits
transcripttools/src		transcripttools/src
BioReaders.c		BioReaders.c
BioReaders.pyx		BioReaders.pyx
BioReaders.so		BioReaders.so
BioReaders_pure.py		BioReaders_pure.py
ORF_gff_reader.py		ORF_gff_reader.py
README.rst		README.rst
RS_Resequencing_Transcript.1.xml		RS_Resequencing_Transcript.1.xml
RS_Resequencing_Transcript_ChickManv2.1.xml		RS_Resequencing_Transcript_ChickManv2.1.xml
RS_Resequencing_Transcript_ChickUCSC.1.xml		RS_Resequencing_Transcript_ChickUCSC.1.xml
RS_Transcript_Gencode13.1.xml		RS_Transcript_Gencode13.1.xml
SeqReaders.py		SeqReaders.py
alignQC.py		alignQC.py
align_template.py		align_template.py
barcode_trimmer.py		barcode_trimmer.py
bin_FL_by_size.py		bin_FL_by_size.py
bin_FL_by_size.py_log		bin_FL_by_size.py_log
bin_FL_by_size_IsoSeq.py		bin_FL_by_size_IsoSeq.py
calc_loading_P1.py		calc_loading_P1.py
chimera_finder.py		chimera_finder.py
classify_barcode.py		classify_barcode.py
clean_primer_match.py		clean_primer_match.py
clean_raw_csv.py		clean_raw_csv.py
compare_fullPass_fullLength.py		compare_fullPass_fullLength.py
count_chimera_rate.py		count_chimera_rate.py
count_homopolymer.py_log		count_homopolymer.py_log
custom_barcode_primers_forward.fa		custom_barcode_primers_forward.fa
custom_barcode_primers_reverse.fa		custom_barcode_primers_reverse.fa
eval_accuracy_by_gmap.py		eval_accuracy_by_gmap.py
eval_cDNApipe_results.py		eval_cDNApipe_results.py
eval_cDNApipe_results_IsoSeq.py		eval_cDNApipe_results_IsoSeq.py
eval_chemistry_bias_from_GMAP_SAM.py		eval_chemistry_bias_from_GMAP_SAM.py
eval_refmap_by_blasr.py		eval_refmap_by_blasr.py
extract_run_sample_metadata.py		extract_run_sample_metadata.py
fetch_sequence.py		fetch_sequence.py
file_exists.py		file_exists.py
fluid_barcode_identification.py_log		fluid_barcode_identification.py_log
generate_baxCCS_bash_Sequel.py		generate_baxCCS_bash_Sequel.py
generate_cDNApipe_bash.py		generate_cDNApipe_bash.py
generate_cDNApipe_bash_IsoSeq.py		generate_cDNApipe_bash_IsoSeq.py
generate_classify_bash_Sequel.py		generate_classify_bash_Sequel.py
get_noFL.py_log		get_noFL.py_log
get_noFL_for_pbtranscript.py		get_noFL_for_pbtranscript.py
get_num_passes.py		get_num_passes.py
get_percent_flnc_under1kb.py_log		get_percent_flnc_under1kb.py_log
get_unique_seqs.py		get_unique_seqs.py
gff3_to_collapsed.py		gff3_to_collapsed.py
grab_nonCCS_subreads.py		grab_nonCCS_subreads.py
hmmer_wrapper.py		hmmer_wrapper.py
longest_perZMW.py		longest_perZMW.py
make_bax2bam.py_log		make_bax2bam.py_log
make_ccs_sh.py_log		make_ccs_sh.py_log
make_primer_match_script.sh		make_primer_match_script.sh
make_runs_from_smrtpipe.py		make_runs_from_smrtpipe.py
plot_FL_by_in.py		plot_FL_by_in.py
plot_FL_seqlengths.py_log		plot_FL_seqlengths.py_log
plot_seqlengths.py		plot_seqlengths.py
plot_seqlengths_from_summary.py		plot_seqlengths_from_summary.py
plot_seqlengths_grouped.py		plot_seqlengths_grouped.py
quickSW.py		quickSW.py
rarefaction.py		rarefaction.py
report_primer_match_perZMW.py		report_primer_match_perZMW.py
run_pm.py		run_pm.py
run_pm_IsoSeq.py		run_pm_IsoSeq.py
sam_to_bam.py		sam_to_bam.py
separate_by_barcode.py_log		separate_by_barcode.py_log
setup.py		setup.py
setup_smrtpipe.py		setup_smrtpipe.py
smrtpipe.sh		smrtpipe.sh
stat_seqlength.py		stat_seqlength.py
summarize_aligned_sam_stats.py		summarize_aligned_sam_stats.py
summarize_primer_info.py		summarize_primer_info.py
symlink_images.py_log		symlink_images.py_log
tabulate_full_cDNA_eval.py		tabulate_full_cDNA_eval.py
tabulate_full_cDNA_eval_IsoSeq.py		tabulate_full_cDNA_eval_IsoSeq.py
tabulate_full_cDNA_eval_Sequel.py		tabulate_full_cDNA_eval_Sequel.py
tally_ccs_by_movie.py_log		tally_ccs_by_movie.py_log
tally_sizebin_barcode.py_log		tally_sizebin_barcode.py_log
test.py		test.py
transcript_gencode13.3.xml		transcript_gencode13.3.xml
update_symlink_to_pbi.py_log		update_symlink_to_pbi.py_log
validate_53seen_against_Gencode.py		validate_53seen_against_Gencode.py
validate_file_exists.py		validate_file_exists.py