Forum: Bioinformatics
10-19-2016, 09:49 AM
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Replies: 1
Views: 1,150
Improving bacterial genome assembly
Deall seqanswers community, hope you are all doing well.
I have sequenced and assembled 8 bacterial genomes of the same species.
The initial assembly was constructed using paired-end reads from a...
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Forum: Bioinformatics
01-29-2015, 06:08 PM
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Replies: 7
Views: 4,596
Hi,
If you have a CLC Genomics Workbench...
Hi,
If you have a CLC Genomics Workbench around, you can generate what they call a "detailed mapping report" of your reads-Reference genome. It will show the fraction of genome covered by your...
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Forum: Illumina/Solexa
12-22-2014, 08:06 PM
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Replies: 14
Views: 3,330
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Forum: Illumina/Solexa
12-22-2014, 06:58 PM
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Replies: 14
Views: 3,330
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Forum: Illumina/Solexa
12-22-2014, 06:56 PM
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Replies: 14
Views: 3,330
Please see this link...
Please see this link http://www.ncbi.nlm.nih.gov/assembly/docs/submission/#ex1
(Submitting a haploid assembly: submitting WGS contigs only)
The quality score file is not a must.
I saw that they...
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Forum: Illumina/Solexa
12-22-2014, 05:30 PM
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Replies: 14
Views: 3,330
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Forum: Illumina/Solexa
12-20-2014, 08:20 AM
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Replies: 14
Views: 3,330
Generate a base level quality score file
Dear all,
Would anyone help me know how to generate/extract a base level quality score file from fastq files that can be used to submit data at NCBI.
The file should look like this:
>contig0001...
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Forum: RNA Sequencing
12-20-2014, 07:54 AM
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Replies: 48
Views: 9,887
By now, you've got many suggestions from more...
By now, you've got many suggestions from more experienced readers. You are lucky because you've just got to sit down and think of which option to use.
I am not familiar wth RNA seq projects, but...
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Forum: RNA Sequencing
12-18-2014, 06:49 PM
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Replies: 48
Views: 9,887
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Forum: Bioinformatics
12-01-2014, 02:08 AM
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Replies: 14
Views: 7,858
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Forum: Bioinformatics
12-01-2014, 01:59 AM
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Replies: 14
Views: 7,858
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Forum: Bioinformatics
09-03-2014, 12:14 PM
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Replies: 0
Views: 862
Adding annotations on concatenated genes
Dear all,
I would like to use ACT to visualize a number of concatenated genes and compare theme between a number of isolates (Say a reference Vs assembled and annotated isolates).
I was able to...
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Forum: Bioinformatics
05-30-2014, 03:11 AM
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Replies: 2
Views: 1,701
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Forum: MGISEQ (FKA Complete Genomics)
05-08-2014, 11:48 PM
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Replies: 6
Views: 10,530
It is advisable to contact CLC as suggested by...
It is advisable to contact CLC as suggested by @Genomax. In my experience, the De Novo assembly using CLC Genomic workbench takes ~2 h for 3 GB data (let a total of 5-7 different samples). I suspect...
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Forum: General
04-14-2014, 03:39 AM
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Replies: 1
Views: 2,526
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Forum: General
04-01-2014, 06:24 AM
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Replies: 6
Views: 2,156
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Forum: General
04-01-2014, 05:11 AM
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Replies: 6
Views: 2,156
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Forum: Illumina/Solexa
03-31-2014, 05:38 PM
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Replies: 17
Views: 12,436
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Forum: General
03-27-2014, 07:30 AM
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Replies: 6
Views: 2,156
Region of zero coverage
Dear all,
I have been sequencing some samples and found something that is new for me.
After sequencing using Miseq, I usually align reads using CLC Genomic Workbench and from there, I get the...
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Forum: Sample Prep / Library Generation
02-21-2014, 04:46 AM
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Replies: 9
Views: 2,981
I would recommend you then to choose "Generate...
I would recommend you then to choose "Generate FASTQ" workflow and analyze data using a third-party software by yourself.
I have a small experience with CLC Genomic Workbench and on it I manually...
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Forum: Bioinformatics
02-20-2014, 07:54 PM
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Replies: 2
Views: 1,443
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Forum: Sample Prep / Library Generation
02-20-2014, 07:48 PM
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Replies: 9
Views: 2,981
[QUOTE=exo;132982]
I mean theoretically, this...
[QUOTE=exo;132982]
I mean theoretically, this should be possible since both kits use the same indices and adapters (correct me if im wrong please :) ).
I may be misreading your statement, but I...
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Forum: Illumina/Solexa
02-20-2014, 07:21 PM
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Replies: 17
Views: 12,436
Dear Colleagues,
Thank you for your...
Dear Colleagues,
Thank you for your contributions!
I want just to close to update you on what happened.
I got assistance from Illumina and they just created another sheet for me.
In fact, they...
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Forum: Illumina/Solexa
02-03-2014, 11:45 PM
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Replies: 17
Views: 12,436
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Forum: Illumina/Solexa
02-03-2014, 07:00 PM
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Replies: 17
Views: 12,436
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