Releases: ahs2202/ouro-tools
[v0.2.8] Bioconda integration tested
[v0.2.7] conda packaging tested
[v0.2.7] conda packaging tested
The first released version of Ouro-Tools (utilized for building Mouse Splicing Atlas)
%% RELEASE NOTE %%
2023-08-10 16:41:24
draft version of 'LongFilterNSplit' function completed
2023-08-24 14:40:47
draft version of 'LongExtractBarcodeFromBAM' and 'LongCreateReferenceSizeDistribution' function completed.
2023-08-30 23:51:34
draft version of 'LongExportNormalizedCountMatrix' function was completed. chromosome-level multiprocessing is used, and size-distribution-normalized count matrix can be exported for multiple size ranges of interest, along with the raw count matrix.
2023-09-19 12:38:25
utility functions 'DeduplicateBAM' and 'SplitBAMs' were implemented. Currently, 'DeduplicateBAM' function selects the longest read with the same CB-UMI pair for each bucket (unique CB-UMI attachment location on the genome).
2023-09-27 23:12:53
'LongExportNormalizedCountMatrix' function was modified for more accurate identification of specific transcript using re-alignment (TES matching, filtering alignment with excessive soft-clipping, and strand-specific assignment)
Also, a typo in graph labels were fixed.
2023-10-11 01:08:56
'LongExportNormalizedCountMatrix' function was modified for exporting count features excluding internal poly-A primed reads, which can be helpful for alternative splicing analysis. Most features, excluding variant information features, will be exported with/without internal polyA primed reads if possible.
2023-11-02 23:00:23
'LongFilterNSplit' : Ouro-Enrich applied samples can be now processed with 'LongFilterNSplit' with 'flag_recover_original_molecule_before_self_circularization_and_digestion' flag turned on.
2023-11-03 23:32:31
'LongFilterNSplit' : now molecules with poly A at both ends can be detected and filtered accordingly by default. Also, subsampling of input FASTQ file for exploratory analysis is now supported.
2024-01-10 21:30:02
'LongExportNormalizedCountMatrix' : ('analysis_statistics.tsv.gz' output) now full-length read statistics will be exported for each feature .