Forum: Open Genomics Engine Project
07-22-2016, 06:41 AM
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Replies: 15
Views: 62,460
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Forum: Bioinformatics
08-21-2015, 07:06 AM
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Replies: 9
Views: 6,519
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Forum: Bioinformatics
01-03-2014, 01:04 AM
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Replies: 5
Views: 4,081
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Forum: Bioinformatics
01-02-2014, 01:37 AM
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Replies: 0
Views: 1,263
Experiences with the new Human GRC38
Happy New year 2014 All,
We have been running some tests with the new GRC38 and our aligner, Novoalign. It seems there are some alternate sequences that are in there which Im assuming are for...
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Forum: Bioinformatics
04-26-2013, 08:10 AM
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Replies: 94
Views: 161,262
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Forum: Bioinformatics
04-16-2013, 11:25 AM
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Replies: 14
Views: 6,960
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Forum: Bioinformatics
04-13-2013, 07:34 PM
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Replies: 94
Views: 161,262
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Forum: Bioinformatics
04-12-2013, 03:54 PM
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Replies: 1
Views: 1,357
Hi
We typically would like to filter out...
Hi
We typically would like to filter out ambiguous mapping reads when calling variants. Novoalign scores all of the cases above with a mapping quality of zero. In most cases our users usually set...
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Forum: Bioinformatics
10-08-2012, 07:25 AM
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Replies: 7
Views: 3,065
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Forum: Bioinformatics
09-24-2012, 07:48 AM
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Replies: 17
Views: 6,856
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Forum: Bioinformatics
09-24-2012, 07:43 AM
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Replies: 7
Views: 3,236
Hi Allenyu
Try adding " --hdrhd 4" to your...
Hi Allenyu
Try adding " --hdrhd 4" to your novoalign command in case there is more than 1 byte difference between the read names of a set of paired reads.
Also note that read1 and read2 should...
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Forum: Bioinformatics
09-18-2012, 10:22 AM
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Replies: 0
Views: 1,590
Experiences with Novosort
Hi, We recently had a user send us information on their experience with novosort on large BAM files.
Picard was previously used for sorting, but (due to the underlying Java virtual machine?)...
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Forum: Bioinformatics
07-16-2012, 08:26 PM
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Replies: 13
Views: 4,198
I think it's worth noting here that GSNAP has a...
I think it's worth noting here that GSNAP has a built-in RNASeq model that allows the program to map reads to splice junctions whereas this is totally missing in novoalign as a dedicated feature.
A...
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Forum: Open Genomics Engine Project
06-11-2012, 10:49 AM
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Replies: 6
Views: 9,861
This is a good point. How does openge make it...
This is a good point. How does openge make it easier us to run good genomics workflows. Perhaps an easyrun function for exome, RNASeq,etc, analysis will be a great thing to have in this system.
...
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Forum: Open Genomics Engine Project
06-11-2012, 10:48 AM
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Replies: 2
Views: 16,116
OpenGE on Redhat
Hi
I am trying to get the openGE binaries working on Redhat enterprise machines. openge fails with the following error:
openge: symbol lookup error: openge: undefined symbol:...
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Forum: Bioinformatics
04-23-2012, 01:50 PM
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Replies: 8
Views: 2,113
This is a fairly old version of novoalign that...
This is a fairly old version of novoalign that was used in the comparison. In that older version the gap extension penalty of 15 was much higher than BWA or Bowtie's 5. In our latest versions we...
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Forum: Bioinformatics
04-20-2012, 07:13 PM
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Replies: 6
Views: 2,539
Hi Slp and Gen2007
The short answer is no we...
Hi Slp and Gen2007
The short answer is no we have not done an extensive comparison of the two systems. Bismark is alignment+methylation caller so the best way to compare would be against...
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Forum: Bioinformatics
04-07-2012, 09:59 PM
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Replies: 3
Views: 4,106
Hi Luca
Great tool. Any plans to support...
Hi Luca
Great tool. Any plans to support novoalign in SEAL? We think it would be a great addition to your toolset and we can make a good case why it should be added as an alternative to BWA...
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Forum: Bioinformatics
01-17-2012, 07:59 AM
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Replies: 26
Views: 16,322
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Forum: Bioinformatics
01-16-2012, 12:32 AM
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Replies: 6
Views: 7,115
The "-R" option is for your reference genome...
The "-R" option is for your reference genome fasta file. This is not to be confused with the refseq ROD for GATK (http://www.broadinstitute.org/gsa/wiki/index.php/RefSeq)
I think you will need to...
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Forum: Bioinformatics
01-04-2012, 09:13 PM
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Replies: 23
Views: 10,873
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Forum: Bioinformatics
01-04-2012, 05:07 PM
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Replies: 23
Views: 10,873
Hi
You will need to specify two input files...
Hi
You will need to specify two input files for novoalign to do a paired-end Illumina alignment e.g.
novoalign -d database -f file1.fastq file2.fastq [..other options..]
The order of the...
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Forum: Bioinformatics
12-18-2011, 07:32 AM
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Replies: 2
Views: 2,667
Try the Useq http://useq.sourceforge.net ...
Try the Useq http://useq.sourceforge.net MakeTranscriptome tool.
You can then align all your reads and then use the http://useq.sourceforge.net/cmdLnMenus.html#SamTranscriptomeParser...
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Forum: Bioinformatics
12-15-2011, 05:20 PM
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Replies: 3
Views: 1,886
Take a look at our protocol at...
Take a look at our protocol at http://www.novocraft.com/wiki/tiki-index.php?page_ref_id=35 . The output is a SAM file that may be used for calculating expression, gene fusions and splice junctions.
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Forum: Bioinformatics
12-15-2011, 07:23 AM
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Replies: 11
Views: 4,557
VCF version 4 contains this information if you...
VCF version 4 contains this information if you call your variants with mpileup-bcftools or the GATK UnifiedGenotyper. Have a look at the docs but note that both programs do not produce the exact same...
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