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Search: Posts Made By: Sergioo
Forum: Bioinformatics 10-19-2016, 09:49 AM
Replies: 1
Views: 1,164
Posted By Sergioo
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...
Forum: Bioinformatics 01-29-2015, 06:08 PM
Replies: 7
Views: 4,657
Posted By Sergioo
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...
Forum: Illumina/Solexa 12-22-2014, 08:06 PM
Replies: 14
Views: 3,379
Posted By Sergioo
Thumbs up Thanks for your recommendations, I will go on...

Thanks for your recommendations, I will go on with "b".
Forum: Illumina/Solexa 12-22-2014, 06:58 PM
Replies: 14
Views: 3,379
Posted By Sergioo
At least that is the way I understood :) I'm...

At least that is the way I understood :)
I'm sorry if I am confusing you all
Thanks
Forum: Illumina/Solexa 12-22-2014, 06:56 PM
Replies: 14
Views: 3,379
Posted By Sergioo
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...
Forum: Illumina/Solexa 12-22-2014, 05:30 PM
Replies: 14
Views: 3,379
Posted By Sergioo
Thanks all for your comments, I am really stuck...

Thanks all for your comments, I am really stuck on this one. The following quoted message is from NCBI
"Sequence quality is used in Sanger sequencing. For the high throughput sequencing
methods,...
Forum: Illumina/Solexa 12-20-2014, 08:20 AM
Replies: 14
Views: 3,379
Posted By Sergioo
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...
Forum: RNA Sequencing 12-20-2014, 07:54 AM
Replies: 48
Views: 9,971
Posted By Sergioo
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...
Forum: RNA Sequencing 12-18-2014, 06:49 PM
Replies: 48
Views: 9,971
Posted By Sergioo
What do you mean exactly by sequence type? Maybe...

What do you mean exactly by sequence type? Maybe those assigned from MLST typing?
Forum: Bioinformatics 12-01-2014, 02:08 AM
Replies: 14
Views: 7,992
Posted By Sergioo
IMO, science does not need such committees and...

IMO, science does not need such committees and those remarks are less helpful.
Believe me, Ph.D student that perform well are not those with harsh advisors.
Forum: Bioinformatics 12-01-2014, 01:59 AM
Replies: 14
Views: 7,992
Posted By Sergioo
Had an impression that I was reading my...

Had an impression that I was reading my Supervisor's email.
Hope you didn't offend the guy who asked :-)
Forum: Bioinformatics 09-03-2014, 12:14 PM
Replies: 0
Views: 881
Posted By Sergioo
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...
Forum: Bioinformatics 05-30-2014, 03:11 AM
Replies: 2
Views: 1,714
Posted By Sergioo
Hello Kyubi, Did you came up with a solution to...

Hello Kyubi,
Did you came up with a solution to your joined contigs?
If I remember, the "contig joining tool" of CLC is still in Beta version, thus somehow not yet sure!
If it is not yet late,...
Forum: MGISEQ (FKA Complete Genomics) 05-08-2014, 11:48 PM
Replies: 6
Views: 10,773
Posted By Sergioo
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...
Forum: General 04-14-2014, 03:39 AM
Replies: 1
Views: 2,549
Posted By Sergioo
I was surprised to see this post here (maybe not...

I was surprised to see this post here (maybe not the right place) but would have been more than happy to see comments from Ph.D students.
Roughly, Ph.D is tough for many and on my own experience, I...
Forum: General 04-01-2014, 06:24 AM
Replies: 6
Views: 2,194
Posted By Sergioo
Thanks for your reply, Please see attached Pic 1...

Thanks for your reply, Please see attached Pic 1 & 2., the deletion covers ~100,000 bp (The genome is ~3000 Mb) but in different area/regions. Please note that some regions correspond to genes that...
Forum: General 04-01-2014, 05:11 AM
Replies: 6
Views: 2,194
Posted By Sergioo
Thanks for your reply, but how do we know if it...

Thanks for your reply, but how do we know if it is a deletion or poor assembly/mapping ?:confused:
Forum: Illumina/Solexa 03-31-2014, 05:38 PM
Replies: 17
Views: 12,573
Posted By Sergioo
You are right. Thanks for your contribution

You are right. Thanks for your contribution
Forum: General 03-27-2014, 07:30 AM
Replies: 6
Views: 2,194
Posted By Sergioo
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...
Forum: Sample Prep / Library Generation 02-21-2014, 04:46 AM
Replies: 9
Views: 3,031
Posted By Sergioo
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...
Forum: Bioinformatics 02-20-2014, 07:54 PM
Replies: 2
Views: 1,469
Posted By Sergioo
Another easy option is, to allow Miseq itself...

Another easy option is, to allow Miseq itself assemble your run. And you will get contigs as results of your run! Hope it helps
Forum: Sample Prep / Library Generation 02-20-2014, 07:48 PM
Replies: 9
Views: 3,031
Posted By Sergioo
[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...
Forum: Illumina/Solexa 02-20-2014, 07:21 PM
Replies: 17
Views: 12,573
Posted By Sergioo
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...
Forum: Illumina/Solexa 02-03-2014, 11:45 PM
Replies: 17
Views: 12,573
Posted By Sergioo
I have created the sample sheet using the IEM as...

I have created the sample sheet using the IEM as it is usually done.
Create sample sheet------Other-----Generate FASTQ only-----select the plate------and check whether everything was ok, then...
Forum: Illumina/Solexa 02-03-2014, 07:00 PM
Replies: 17
Views: 12,573
Posted By Sergioo
FASTQ files was missing and CompletedJobInfo.xml...

FASTQ files was missing and CompletedJobInfo.xml as well.
By searching deep into the folders, I found that the sample sheet was not recognized by the Miseq control software (for unknown reason, it...
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