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上传时间:2017-06-02 16:32:49
Version: v2.9
Release Date: 17-Nov-2016


New Features / Enhancements:
1. RNA alignment has been optimized for speed by using optimal transcriptome index. This has resulted in 15 to 35 % reduction in alignment time depending on read length and alignment type.
2. SNP detection has been optimized to handle large number of samples (hundreds of samples). In a 200 sample experiment, this change has resulted in a 10% reduction in SNP detection time.
3. Motif Scan step has been optimized for speed. This has resulted in a fixed reduction in motif scan time depending on the organism-build of the experiment.
4. In genome browser, experiment name has been removed from track titles for the tracks belonging to the currently active experiment. This makes the track titles cleaner, readable and avoids title truncation issues with long experiment names.
5. Logging system has been enhanced to provide more details on threads usage which will help in faster diagnosis of customer issues.
6. Sample import has been optimized to handle samples containing reads from sequences which are not part of the build. This change is an extension to the changes done in the previous release.
7. In local realignment, a new threshold parameter 'minimum percent of reads supporting candidate haplotype' has been added.
8. In the wizard for replicate analysis, UI has been enhanced for the paired T-Test column reordering page. In this page it is now possible to sort individual columns, which comes in handy when pairing large number of samples.

Bug Fixes:
1. In case of cancelling annotation download from annotation manager, disk space was not cleared in some cases. This has been handled now.
2. When performing adapter trimming with multiple input files for one sample, only the first file was trimmed. This has been fixed now.
3. In the exported VCF files, GQ field is renamed to NR (Phred score corresponding to probability that SNP call is not reference).
4. In MeDIP-Seq experiments, DMR detection was giving incorrect results in some cases. This has been fixed.
5. While creating genes and transcript annotations from gff file, exons were not sorted properly for negative strand. This has been corrected.
6. While creating genes and transcript annotations from gff file, sequence aliases were not handled properly potentially resulting in incorrect alias mappings. This has been fixed by introducing additional constraints in the wizard.
7. On Windows 7, R editor was not working after product upgrade. This has been fixed.
8. Scan Motif gave different results across runs. This has been fixed.
9. Motif import failed for some motifs. This has been fixed.
10. Filtering peak regions sometimes failed. This has been fixed.
11. Launching Venn diagram on targeted genes lists was failing with an unknown error dialog. This has been fixed.
12. Importing builds with large number of sequences (in thousands) was failing and causing annotation manager to freeze. This has been fixed by introducing a higher cut-off on the number of sequences a build can have to 500.
13. When a filtered SNP multi sample report was exported to VCF, only first sample's fields were present. This has been fixed.
14. With imported VCF files, SNP effect analysis was failing sometimes. This has been fixed.