Forum: Bioinformatics
08-05-2014, 01:13 AM
|
|
Replies: 13
Views: 5,073
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...
|
|
Forum: Bioinformatics
08-05-2014, 12:53 AM
|
|
Replies: 13
Views: 5,073
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...
|
|
Forum: Bioinformatics
08-05-2014, 12:46 AM
|
|
Replies: 13
Views: 5,073
|
|
Forum: Bioinformatics
08-05-2014, 12:42 AM
|
|
Replies: 13
Views: 5,073
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...
|
|
Forum: Bioinformatics
08-04-2014, 03:43 AM
|
|
Replies: 13
Views: 5,073
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...
|
|
Forum: Bioinformatics
07-31-2014, 03:59 AM
|
|
Replies: 13
Views: 5,073
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...
|
|
Forum: Bioinformatics
03-25-2014, 12:28 AM
|
|
Replies: 1
Views: 965
|
|
Forum: Bioinformatics
03-21-2014, 06:20 AM
|
|
Replies: 6
Views: 1,797
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...
|
|
Forum: Bioinformatics
03-21-2014, 06:10 AM
|
|
Replies: 6
Views: 1,797
|
|
Forum: Bioinformatics
03-19-2014, 12:29 AM
|
|
Replies: 6
Views: 1,797
|
|
Forum: Bioinformatics
01-07-2014, 02:40 AM
|
|
Replies: 366
Views: 204,735
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...
|
|
Forum: Bioinformatics
08-08-2012, 04:24 AM
|
|
Replies: 3
Views: 1,317
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
|
|
Forum: Bioinformatics
07-25-2012, 01:01 AM
|
|
Replies: 7
Views: 4,711
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...
|
|
Forum: Bioinformatics
07-21-2012, 01:57 AM
|
|
Replies: 5
Views: 3,407
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...
|
|
Forum: Bioinformatics
07-21-2012, 01:54 AM
|
|
Replies: 7
Views: 4,711
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...
|
|
Forum: Bioinformatics
07-08-2012, 11:46 PM
|
|
Replies: 26
Views: 15,747
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.
--...
|
|
Forum: Bioinformatics
07-08-2012, 11:31 PM
|
|
Replies: 1
Views: 2,518
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...
|
|
Forum: Bioinformatics
05-27-2012, 11:51 PM
|
|
Replies: 14
Views: 5,065
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...
|
|
Forum: Bioinformatics
04-20-2012, 02:38 AM
|
|
Replies: 40
Views: 21,331
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...
|
|
Forum: Bioinformatics
01-12-2012, 04:38 AM
|
|
Replies: 2
Views: 3,056
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
...
|
|
Forum: Bioinformatics
01-12-2012, 04:35 AM
|
|
Replies: 12
Views: 3,329
|
|
Forum: Bioinformatics
01-10-2012, 12:51 AM
|
|
Replies: 3
Views: 2,399
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...
|
|
Forum: Bioinformatics
11-30-2011, 03:44 AM
|
|
Replies: 2
Views: 2,391
|
|
Forum: Bioinformatics
11-28-2011, 11:39 PM
|
|
Replies: 2
Views: 2,503
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...
|
|
Forum: Bioinformatics
11-28-2011, 12:07 AM
|
|
Replies: 2
Views: 2,503
|
