SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 25 of 249
Search took 0.06 seconds.
Search: Posts Made By: zee
Forum: Open Genomics Engine Project 07-22-2016, 05:41 AM
Replies: 14
Views: 40,605
Posted By zee
This post seems pretty out-of-date.

This post seems pretty out-of-date.
Forum: Bioinformatics 08-21-2015, 06:06 AM
Replies: 9
Views: 4,414
Posted By zee
We have just released a new program in the Novo*...

We have just released a new program in the Novo* suite that facilitates PacBio read error correction with Novoalign. We used this strategy - similar to LSC - to assemble the first draft...
Forum: Bioinformatics 01-03-2014, 12:04 AM
Replies: 5
Views: 2,442
Posted By zee
Welcome to the world of OSS.

Welcome to the world of OSS.
Forum: Bioinformatics 01-02-2014, 12:37 AM
Replies: 0
Views: 999
Posted By zee
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...
Forum: Bioinformatics 04-26-2013, 07:10 AM
Replies: 94
Views: 138,449
Posted By zee
Congratulations Shi on getting Subread published...

Congratulations Shi on getting Subread published and I think the theory of it is quite interesting.
Subread does an interesting comparison of aligners in Table 2 of the publication. This table shows...
Forum: Bioinformatics 04-16-2013, 10:25 AM
Replies: 14
Views: 4,489
Posted By zee
I like this idea a lot as well. We should try it...

I like this idea a lot as well. We should try it sometime.
Forum: Bioinformatics 04-13-2013, 06:34 PM
Replies: 94
Views: 138,449
Posted By zee
GCAT is great because it allows you to run and...

GCAT is great because it allows you to run and submit your own datasets for public scrutiny. We are going to make good use of it.
Forum: Bioinformatics 04-12-2013, 02:54 PM
Replies: 1
Views: 1,068
Posted By zee
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...
Forum: Bioinformatics 10-08-2012, 06:25 AM
Replies: 7
Views: 2,403
Posted By zee
It is most likely that one piece of software is...

It is most likely that one piece of software is not going to bring it all together. You will need some help integrating and maintaining a very good pipeline(s) for processing sequence data.

For...
Forum: Bioinformatics 09-24-2012, 06:48 AM
Replies: 17
Views: 5,464
Posted By zee
If you have the Bowtie2 PE result then perhaps do...

If you have the Bowtie2 PE result then perhaps do "samtools flagstat" on the Bowtie2 BAM file to determine how many reads alignn, how many proper pairs to expect,etc. You may also infer the insert...
Forum: Bioinformatics 09-24-2012, 06:43 AM
Replies: 7
Views: 2,287
Posted By zee
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...
Forum: Bioinformatics 09-18-2012, 09:22 AM
Replies: 0
Views: 1,192
Posted By zee
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?)...
Forum: Bioinformatics 07-16-2012, 07:26 PM
Replies: 13
Views: 3,531
Posted By zee
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...
Forum: Open Genomics Engine Project 06-11-2012, 09:49 AM
Replies: 6
Views: 5,744
Posted By zee
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.
...
Forum: Open Genomics Engine Project 06-11-2012, 09:48 AM
Replies: 2
Views: 12,224
Posted By zee
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:...
Forum: Bioinformatics 04-23-2012, 12:50 PM
Replies: 8
Views: 1,607
Posted By zee
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...
Forum: Bioinformatics 04-20-2012, 06:13 PM
Replies: 6
Views: 1,896
Posted By zee
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...
Forum: Bioinformatics 04-07-2012, 08:59 PM
Replies: 3
Views: 3,517
Posted By zee
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...
Forum: Bioinformatics 01-17-2012, 06:59 AM
Replies: 26
Views: 13,058
Posted By zee
You definitely need @RG records in your file. ...

You definitely need @RG records in your file.

To check this do
samtools view -H file.bam | grep ^@RG
This will probably yield no results.

Use Picard to add a readgroup to your file e.g.
...
Forum: Bioinformatics 01-15-2012, 11:32 PM
Replies: 6
Views: 6,429
Posted By zee
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...
Forum: Bioinformatics 01-04-2012, 08:13 PM
Replies: 23
Views: 8,819
Posted By zee
OK, I can understand what you're doing here but ...

OK, I can understand what you're doing here but if your $FILE represents "read_1 read_2" then your output BAM file will be called "read_1 read_2".bam which is going to cause some problems for you....
Forum: Bioinformatics 01-04-2012, 04:07 PM
Replies: 23
Views: 8,819
Posted By zee
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...
Forum: Bioinformatics 12-18-2011, 06:32 AM
Replies: 2
Views: 2,169
Posted By zee
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...
Forum: Bioinformatics 12-15-2011, 04:20 PM
Replies: 3
Views: 1,516
Posted By zee
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.
Forum: Bioinformatics 12-15-2011, 06:23 AM
Replies: 11
Views: 3,430
Posted By zee
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...
Showing results 1 to 25 of 249

 


All times are GMT -8. The time now is 11:44 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO