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addressing a number of bug reports. Most prominently changes include: 1) Added a testsuite to verify the output on a variety of error identification worksheets SAM files. *Beta* Version 1.5 Posted on August 14th 2014 by

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Timo Lassmann Version 1.5 is addressing several issues with the now 4 year old original version of error identification sat practice SAMstat. Most prominently changes include: 1) Better support for long reads.Version 1.5 uses a simple hidden Markov model to calculate the positon specific nucleotide over-representation profiles. 2) error identification big exercise 1 Better visualization using the excellent Chartjs library for drawing plots. Version 1.09 Posted on July 8th 2013 by Timo Lassmann Version 1.09: fixed compilation issues on Ubuntu Linux. Posted on March 23th 2011 by Timo Lassmann Version 1.08 allows users to print a summary over multiple input files. Additionally several several minor bugs were fixed. Introduction

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Posted on September 21th 2010 by Timo Lassmann Next generation sequencing is being applied to understand individual variation, the RNA output of a cell and epigenetic regulation. The millions of sequenced reads are commonly stored in fasta, fastq and after mapping to a reference genome in the alignment / map format (SAM/BAM). To monitor the sequence quality over time and to identify problems it is necessary to report various statistics of the reads at different stages during processing. SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines. SAMStat reports nucleotide composition, length distribution, base quality distribution, mapping statistics, mismatch, insertion and deletion error

faq • rss Community Log In Sign Up Add error identification definition New Post Question: FixMateInformation issue in the process of running sam file statistics picard 0 24 months ago by zengtony743 • 60 Canada zengtony743 • 60 wrote:

Samstat

When I ran FixMateInformation under the picard, it has done with no any error by producing an output. HOwever, in the process of http://samstat.sourceforge.net/ running fixmateinforamtion, at the beginning it showed information like " Ignoring SAM validation error:......" then it turns back to normal until the "done" Is this the normal process for running fixmateinforamtion? I worry about this because there is problem for my downstream process and now I https://www.biostars.org/p/116132/ have to return back to redo upstream process, so I need to be really careful to make sure that every step is right from the early process.. Thank you,   Here is the information I have: commands: $ java -jar FixMateInformation.jar INPUT=MO_136.marked.realigned.bam OUTPUT=MO_136.fixed.bam SO=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true &   Then: [rzeng@qlogin3 reference]$ [Mon Oct 20 10:17:35 EDT 2014] net.sf.picard.sam.FixMateInformation INPUT=[MO_136.marked.realigned.bam] OUTPUT=MO_136.fixed.bam SORT_ORDER=coordinate VALIDATION_STRINGENCY=LENIENT CREATE_INDEX=true    VERBOSITY=INFO QUIET=false COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false [Mon Oct 20 10:17:35 EDT 2014] Executing as rzeng@qlogin3 on Linux 2.6.32-358.18.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_55-mockbuild_2014_04_16_12_11-b00; Picard version: 1.101(1580) INFO    2014-10-20 10:17:35    FixMateInformation    Sorting input into queryname order.   Then:   Ignoring SAM validation error: ERROR: Record 79826696, Read name HWI-ST724:304:HAE4JADXX:1:1114:12017:81845, MAPQ should be 0 for unmapped read. Ignoring SAM validation error: ERROR: Record 79826697, Read name HWI-ST724:304:HAE4JADXX:1:1115:17901:26956, MAPQ should be 0 for unmapped read. Ignoring SAM validation

download) Code Maturity Stable. Mature code, but feedback is appreciated. Code Released Yes, under GPL v3 or later. Initial Contact Simon Andrews Download Now View our tutorial video FastQC aims to provide a simple way to http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis. The main functions of FastQC are Import of data from BAM, SAM or FastQ files (any variant) Providing a quick overview to error identification tell you in which areas there may be problems Summary graphs and tables to quickly assess your data Export of results to an HTML based permanent report Offline operation to allow automated generation of reports without running the interactive application Documentation A copy of the FastQC documentation is available for you to try before you buy (well download..). Example Reports Good Illumina Data Bad Illumina Data Adapter dimer contaminated run Small error identification sat RNA with read-through adapter Reduced Representation BS-Seq PacBio 454 Changelog 08-03-16: Version 0.11.5 released Fixed the smallRNA adapter sequence so that abundance isn't under-represented in the adapter content plot Fixed a bug in the warn / error code for the per-base sequence content plot Fixed a typo in the documentation for the duplication plot 09-10-15: Version 0.11.4 released Changed the OSX launcher to not rely on the internal JVM framework, but use any command line java which is found Fixed a typo in one of the adapter sequences Fixed a bug which meant that some file extensions weren't removed from report names in non-interactive mode Made the per-tile module not collect any stats if it's disabled in limits.txt Fixed a bug in the calculation of duplication for highly duplicated, ordered files with very small numbers of sequences Fixed an incorrect error flag in the per-base quality module where there were less than 100 observations in a read group 25-3-15: Version 0.11.3 released Fixed a bug when disabling the per-tile plot from limits.txt Fixed a bug which caused the program to continue when processing of multiple files was actually complete Fixed a bug which meant format selection in the interactive application didn't work Added checks for mis-itentifying tile numbers in confusing sample i

 

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