Forum: Bioinformatics
08-05-2014, 12:13 AM
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Replies: 13
Views: 5,849
Hello,
I do understand that the...
Hello,
I do understand that the pre-processing for MiSeq Paired End data is different.
For my data I first assemble the Paired end reads, using PANDAseq. So no need for split_libraries.py
As...
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Forum: Bioinformatics
08-04-2014, 11:53 PM
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Replies: 13
Views: 5,849
The sequencing was done by a third party...
The sequencing was done by a third party sequencing provider (http://www.scigenom.com/).
On requesting them for (1) Adapter sequences, (2) barcode and (3) Primer sequence for assembling the Paired...
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Forum: Bioinformatics
08-04-2014, 11:46 PM
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Replies: 13
Views: 5,849
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Forum: Bioinformatics
08-04-2014, 11:42 PM
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Replies: 13
Views: 5,849
So that means that in the Qiime mapping file I...
So that means that in the Qiime mapping file I can use any barcode sequence, it only has be a unique one for each sample & same for all replicates of a sample ?
According to my understanding of...
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Forum: Bioinformatics
08-04-2014, 02:43 AM
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Replies: 13
Views: 5,849
bump.
For a MiSeq V3 Data set multiple...
bump.
For a MiSeq V3 Data set multiple samples (3 replicate per sample), with barcode used but sequence not available, how to create a meta-data file so the samples can be associated by Qiime with...
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Forum: Bioinformatics
07-31-2014, 02:59 AM
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Replies: 13
Views: 5,849
Regarding Qiime Metadata Mapping File
Hello,
Library specs: Paired End, Read length 150 bp, V3 region 16S rRNA gene
Platform : MiSeq, Illumina
Experiment : Wheat Field, rhizosphere samples, Elevated CO2 and temperature...
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Forum: Bioinformatics
03-24-2014, 11:28 PM
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Replies: 1
Views: 1,240
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Forum: Bioinformatics
03-21-2014, 05:20 AM
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Replies: 6
Views: 2,383
L, Stein 2010 Genome Biology...
L, Stein 2010 Genome Biology (http://genomebiology.com/2010/11/5/207) provides convincing arguments for moving to the cloud.
Secondly in my country wide scale adoption of Computational analysis has...
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Forum: Bioinformatics
03-21-2014, 05:10 AM
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Replies: 6
Views: 2,383
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Forum: Bioinformatics
03-18-2014, 11:29 PM
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Replies: 6
Views: 2,383
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Forum: Bioinformatics
01-07-2014, 01:40 AM
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Replies: 366
Views: 227,853
Adapter Contamination Detection
Hello,
This blog post (pathogenomics.bham.ac.uk/blog/2013/04/adaptor-trim-or-die-experiences-with-nextera-libraries/) is also of relevance here.
I am assembling a Bacterial Genome.
Library...
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Forum: Bioinformatics
08-08-2012, 03:24 AM
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Replies: 3
Views: 1,622
Hello,
I guess, SNP information from CNV...
Hello,
I guess, SNP information from CNV regions can help in genotyping.
That is, information about the Copy number variation in the different alleles of the sample.
--
pg
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Forum: Bioinformatics
07-25-2012, 12:01 AM
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Replies: 7
Views: 5,419
I think the "-genome" is used incorectly, the...
I think the "-genome" is used incorectly, the word "name" should not be there. Only the name of the genome should come after the "-genome" option.
Also the "-chrom" and "-genome" options are...
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Forum: Bioinformatics
07-21-2012, 12:57 AM
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Replies: 5
Views: 3,992
Hello,
Might be RAM issue, Blast2go uses a...
Hello,
Might be RAM issue, Blast2go uses a lot of memory.
For our node with 96 Gb RAM, we still have to split the blast xml results and then run Blast2Go.
Try spliting the xml input and then...
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Forum: Bioinformatics
07-21-2012, 12:54 AM
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Replies: 7
Views: 5,419
Hello,
What all commands did you use?
...
Hello,
What all commands did you use?
For us it took,
22 mins to run the CNVnator tool on a single 3.2 GHz Intel I3 processor with a 4GB DDR3 (1333 Mhz), 2TB Western Digital hard disk and...
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Forum: Bioinformatics
07-08-2012, 10:46 PM
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Replies: 26
Views: 17,135
Hello,
CNVnator is one of the best tools for...
Hello,
CNVnator is one of the best tools for CNV detection, according to my analysis, for a single sample only.
If you have a Tumor normal pair kind of data then FREEC is a good option.
--...
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Forum: Bioinformatics
07-08-2012, 10:31 PM
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Replies: 1
Views: 2,933
Hello,
This is from the CNVnator manual.
...
Hello,
This is from the CNVnator manual.
********
>>>VISUALIZING SPECIFIED REGIONS
./cnvnator -root file.root [-chrom chr_name1 ...] -view bin_size [-ngc]
Once prompted enter a genomic...
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Forum: Bioinformatics
05-27-2012, 10:51 PM
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Replies: 14
Views: 5,974
The Soyabean people do have a custom Repeat...
The Soyabean people do have a custom Repeat Library for it. I got it from here, http://SoyTEdb.org
I use this command,
$RepeatMasker -s -nolow -norna -no_is -gff -lib Glycine_max_TE_lib.fa...
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Forum: Bioinformatics
04-20-2012, 01:38 AM
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Replies: 40
Views: 23,660
Hello,
This is not a direct answer to your...
Hello,
This is not a direct answer to your question, but there is a tool from the Repeat Masker group.
Its called Repeat Modeler, this tool integrates Repeat Scout, RECON and TRF.
It creates a...
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Forum: Bioinformatics
01-12-2012, 03:38 AM
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Replies: 2
Views: 3,525
Hi,
Please take a look at these posts, as...
Hi,
Please take a look at these posts, as this topic has been discussed before.
http://seqanswers.com/forums/showthread.php?t=12361
http://seqanswers.com/forums/showthread.php?t=9480
...
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Forum: Bioinformatics
01-12-2012, 03:35 AM
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Replies: 12
Views: 4,103
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Forum: Bioinformatics
01-09-2012, 11:51 PM
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Replies: 3
Views: 2,885
Hi,
You could look at, ...
Hi,
You could look at,
http://openwetware.org/wiki/Wikiomics:Repeat_finding#RepeatScout
For analysis.
or
Alternatively I would recommend use Repeat-Modeler...
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Forum: Bioinformatics
11-30-2011, 02:44 AM
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Replies: 2
Views: 2,719
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Forum: Bioinformatics
11-28-2011, 10:39 PM
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Replies: 2
Views: 2,882
Solved
Hi,
No you can not use the "consensi.fa" file as the final result file.
I just took the top 500 scaffolds from my input file and ran Repeat Modeler on them.
It worked and produced a...
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Forum: Bioinformatics
11-27-2011, 11:07 PM
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Replies: 2
Views: 2,882
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