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上传时间:2016-09-30 10:11:44
Version: v2.6
Release Date: 20-Jan-2016


New Features / Enhancements:

1. Strand NGS has enhanced support for creating RNA-Seq analysis experiment. In addition to creating the analysis experiment from aligned reads in sam/bam format, or combining existing analysis experiments, a new RNA-Seq analysis experiment can now be created using pre quantified data from a simple text file. This feature is designed for gene-level analysis and will have access to all the downstream functionality in the RNA-Seq workflow.

2. A new normalization method, reads per million (RPM) has been provided in the RNA-Seq analysis workflow.

3. Adapter trimming support using Cutadapt version 1.9.1 has been introduced within the alignment workflow across all experiment types to trim both 5' and 3' adapters.

4. Analysis of targeted sequencing data from amplicon-based panels is now fully supported using a manifest file. Amplicon targets and target specific PCR-primers are automatically parsed from the manifest file for adapter trimming and for targeted alignment of reads against the amplicon targets.

5. Support for unaligned BAM files (unaligned reads in BAM format) is now provided to create an alignment experiment.

6. SV calling algorithm from split reads is further improved by using a clustering approach based on breakpoints. This results in significant reduction in false positives without affecting true positives. In addition, calculations for other split/partial and paired-end reads for each event are modified accordingly.

7. A new parent node is added in the navigator for results of SV caller from split reads. This node can be inspected to see the notes section with information on the parameter values used while running the algorithm.

8. Computation of % masked column in SV output from split reads is made optional and a new parameter is added in Tools → Options, which is unchecked by default.

9. A new "Select All" button is provided in the create interpretation wizard to help in cases where many conditions are present.

10. The approach to create a MBV list from SBV list has been modified to include only those SBVs that do not pass the SNP filters (SBVs passing the SNP filters should be ignored).

11. A new parameter "minimum supporting reads for detecting MBV" has also been introduced in Tools → Options to detect all MBVs that passes this threshold.

12. Local Realignment has been further enhanced. In addition to the threshold on minimum number of reads, minimum % of supporting reads for each haplotype is also added in Tools → Options.

13. In QC manager, now tile and lane quality plots will also work for data from Illumina's new NextSeq instrument.

14. Pipeline manager and annotation manager are now optimized for faster browsing.

15. Both DESeq and DESeq2 R scripts for differential expression analysis can now handle missing values in the read count data. Genes with missing values are excluded from the analysis and this number is reflected in the console output.

16. Logs of each job are now saved in a task-specific manner to allow easy browsing and debugging.

17. It is now possible to e-mail task specific logs directly from the jobs monitor to NGS support team.

18. Support has been provided for user to add and edit annotations to samples, region lists etc from inspectors. The user-specific sample annotations are also propagated to specific output region lists (SNP, CNV and SV) and are also searchable through the search menu.

19. For motif detection using GADEM algorithm, p-value threshold is now exposed in Tools → Options.

20. Several vital statistics parameters such as memory and disk space available, number of threads, cpu load etc are now printed in log file at periodic intervals. These stats can provide a useful way to debug long running jobs.

21. Server related only:

a. In case the samples are not available in the shared drive, additional functionality to upload samples from the local drive is also supported.
b. Jobs monitor has been enhanced to show waiting job position in the job queue.
c. In order to minimise space requirement, logs on the server are compressed and logs older than 60 days are automatically deleted.
d. Server parameters have been optimised to execute long-running jobs smoothly.
e. It is now possible to view and send logs for jobs running on compute nodes from the remote task manager.

Bug Fixes:

1. When two or more gene lists are compared from different experiments for plotting a venn diagram, sometimes few genes are dropped in translation despite having the same underlying gene and transcript model. This has been fixed now.

2. After local realignment, there are chances that the output read list contains reads with CIGAR of the form 'nI' indicating all insertions. Some of the downstream analysis steps would fail due to the presence of these reads. This has been fixed by skipping local realignment of all such reads.

3. The value of "perform split alignment" would not save while editing an existing DNA-Seq pipeline. This has now been fixed.

4. Reads ignored due to too many matches were earlier considered for split alignment there by sometimes resulting in extra unaligned reads in the end. This has now been fixed by ignoring reads with too many matches during split alignment step.

5. YS tag was wrong in reads which have undergone quality-based trimming. This has been fixed.

6. When entity list is imported using excel file (.xls format), last entry in the file will be dropped. This has been fixed now.

7. "Export as VCF" functionality in the right click menu would not work for imported VAL files. This has been fixed now.

________________________________________
Version: v2.5.1
Release Date: 18-Aug-2015


New Features / Enhancements:

1. Local realignment has been enhanced. It is now possible to discard candidate haplotypes with supporting reads less than a cutoff which can be specified in Tools → Options → DNA Variant Analysis → Local Realignment.

2. SV detection from split reads has been optimized for running time.

3. In the output of SV detection from split reads two new columns have been added which specify the breakpoints corresponding to the event reported.

4. A right click menu option has been enabled for targeted CNV output to export the results as VCF files.

5. A new Jython script has been provided to export the output of SV detection from split reads as VCF files.

Bug Fixes:

1. In Methyl-seq experiment, genome browser would not show any reads when zoomed into base level resolution. This has been fixed.

2. Tail distance bias is sometimes incorrectly computed when deletions are present. This has been fixed.

3. Average Mapping Quality for SNPs in the exported VCF file was wrong. This has been fixed.

4. Server edition only:

a. Exporting BAM file would fail when the destination folder requires client-to-server shared folder mapping. This has been fixed.
b. Two RNA alignment jobs running simultaneously on the same compute node might fail due to synchronization issues. This has been fixed.
c. Z-score column was missing in targeted CNV output. This has been fixed.

Known Issues:

1. Server edition only: In a MeDIP-Seq experiment, running multiple MeDIP-Seq analysis jobs (methylation detection and/or DMR analysis) simultaneously might fail due to synchronization. If this happens abandon the experiment and work with a copy of the experiment instead.