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Forum: Bioinformatics 10-09-2016, 05:19 AM
Replies: 674
Views: 172,444
Posted By sebl
coverage stats

Hi,

I would like to calculate the average coverage of some genomes. I used:

bbmap.sh in1=reads_R1.fq in2=reads_R2.fq ref=scaffolds.fasta nodisk covstats=stats.txt covhist=histogram.txt

I get...
Forum: De novo discovery 09-10-2016, 09:44 PM
Replies: 3
Views: 5,642
Posted By sebl
These are isolate libraries. When I BLAST...

These are isolate libraries.

When I BLAST short contigs (<200bp) with high coverage (10'sx), these are often parts of ribosomal genes. When I BLAST contigs of length 200-~500bp, where most of low...
Forum: De novo discovery 09-09-2016, 11:54 PM
Replies: 3
Views: 5,642
Posted By sebl
Minimum contig coverage to keep

Dear all,

I am working on de novo assembly of bacterial genomes. Genomes were sequenced with Miseq 2x250 libs with an average coverage ~40X. Adapters were trimmed with cutadapt by the seq...
Forum: Service Providers 05-02-2016, 04:36 AM
Replies: 5
Views: 4,410
Posted By sebl
Good point, thanks!

Good point, thanks!
Forum: Service Providers 05-02-2016, 01:17 AM
Replies: 5
Views: 4,410
Posted By sebl
Oh, and I mean that lib prep would be included in...

Oh, and I mean that lib prep would be included in the service.
Forum: Service Providers 05-02-2016, 01:06 AM
Replies: 5
Views: 4,410
Posted By sebl
Hi, Thanks for the links. From Genohub: ...

Hi,

Thanks for the links. From Genohub:



So, if I got it right, let's say we are talking about a Miseq run with V2 chemistry. Illumina specs. are . So the sequencer in Genohub would...
Forum: Service Providers 05-01-2016, 04:36 AM
Replies: 5
Views: 4,410
Posted By sebl
Minimum run output and quality

Hello,

I hope this is the right place to ask this.

I was asked to write the terms for a tender for a NGS service provider for our institute.

We aim to work mainly with whole genome...
Forum: Bioinformatics 12-09-2015, 10:27 AM
Replies: 14
Views: 2,589
Posted By sebl
No problem. You keep the thread active so I may...

No problem. You keep the thread active so I may get more replies from people :)

What about Biolinux as OS? Any cons that I should be aware of?

Thanks again.
Forum: Bioinformatics 12-08-2015, 11:34 AM
Replies: 14
Views: 2,589
Posted By sebl
@GenoMax: Indeed. Also, once we set up a...

@GenoMax: Indeed.

Also, once we set up a pipeline for analysis, if it will take one day more to get it done it does not really matter most times, as long as the computer is able to process it in...
Forum: Bioinformatics 12-08-2015, 10:58 AM
Replies: 14
Views: 2,589
Posted By sebl
I should really check on that. Eh, a...

I should really check on that.



Eh, a colleague suggested that I ask for further processors... The max RAM seems to be 512. But it is already considered a very unusual purchase in our...
Forum: Bioinformatics 12-08-2015, 02:22 AM
Replies: 14
Views: 2,589
Posted By sebl
Feedback on workstation for bioinformatics

Dear all,

Following a discussion on a good workstation for bioinformatics work...

We are working on bacterial/plasmids/viruses genomes. Things we are doing at small scale today and that we are...
Forum: Bioinformatics 12-08-2015, 01:48 AM
Replies: 4
Views: 1,593
Posted By sebl
Thank you for the reply. I guess you are...

Thank you for the reply.

I guess you are right and I should work on quality trimming.

Our libraries however were prepared by mechanical shearing of gDNA, not the usual random hexamer protocol...
Forum: Bioinformatics 12-05-2015, 04:01 AM
Replies: 4
Views: 1,593
Posted By sebl
cut 5' and 3' ends of paired-ends reads

Dear all,

I have 2x250 paired-end reads for de novo assembly of bacterial genomes.

The reads were processed with cutadapt to remove Illumina adaptors.

In FastQC I see that I should remove...
Forum: De novo discovery 03-26-2015, 12:31 AM
Replies: 4
Views: 2,447
Posted By sebl
Thank you for the reply. We may...

Thank you for the reply.



We may disregard these regions for now and work on draft genomes instead. I agree that if we would like to have good reference genomes from our collection we would...
Forum: De novo discovery 03-25-2015, 04:07 AM
Replies: 4
Views: 2,447
Posted By sebl
WGS of ~200 bacteria: recommended sequencing type and size

Hello,

We are going to sequence about 180 different strains of bacteria. These strains are all from the same genus but cover about 7 different species.

The idea is to study phylogeny within...
Forum: Illumina/Solexa 01-25-2015, 01:38 PM
Replies: 5
Views: 5,292
Posted By sebl
miseq run troubleshoot and advice on nextera xt library normalization

Hello,

I would like to ask for some advice on normalization of Nextera XT libraries that will be sequenced on Miseq (paired ends 2x150). We got low output (~400K) in one run with our samples...
Forum: Illumina/Solexa 01-22-2015, 12:09 PM
Replies: 7
Views: 4,110
Posted By sebl
Is there any explanation for that? How are you...

Is there any explanation for that? How are you supposed to QC the libraries otherwise?
Forum: Sample Prep / Library Generation 11-03-2014, 05:46 AM
Replies: 0
Views: 2,174
Posted By sebl
Nextera XT library troubleshooting

Hi,

I would like to ask for some help troubleshooting library preparation from bacterial genomes.

We are using Illumina's Nextera XT kit, strictly following the kit's protocol, and even using...
Forum: Bioinformatics 11-02-2014, 04:53 AM
Replies: 2
Views: 1,616
Posted By sebl
Thank you.

Thank you.
Forum: Bioinformatics 10-26-2014, 05:50 AM
Replies: 2
Views: 1,616
Posted By sebl
bioinformatics workstation configuration

Hi,

I know there are already some threads dealing with minimal configuration of a workstation for bioinformatics, but people talk mostly about assembling or mapping speed. I am working on...
Forum: RNA Sequencing 08-03-2014, 10:53 PM
Replies: 1
Views: 1,548
Posted By sebl
I should mention that we'll use ScriptSeq...

I should mention that we'll use ScriptSeq Complete Kit from Epicentre to deplet rRNA and build RNA libraries.
Forum: RNA Sequencing 08-03-2014, 10:03 PM
Replies: 1
Views: 1,548
Posted By sebl
How much DNA contamination "allowed"?

Hi,

We're going to do a RNA-SEQ experiment (with Nextseq 500) with bacterial RNA for differential gene expression. We have cells lysed and frozen in TRIZOL, and now we're using ZYMO's Direct-Zol...
Forum: Illumina/Solexa 03-02-2014, 04:40 AM
Replies: 0
Views: 1,280
Posted By sebl
Homogenization in Nextera DNA prep kit

Hi,

We are going to use Nextera DNA prep kits for a Miseq run for the first time in our lab. We lack a "high speed" plate shaker at the moment, and it may take some time to get one.

Does anyone...
Forum: Bioinformatics 03-01-2014, 09:41 PM
Replies: 6
Views: 1,211
Posted By sebl
I meant to search for gene sized sequences. ...

I meant to search for gene sized sequences.

The question is if there is a script to allow automatic BLAST search of a list of sequence queries in a list of genome files, and returns the results...
Forum: Bioinformatics 03-01-2014, 01:45 PM
Replies: 6
Views: 1,211
Posted By sebl
I meant search by similarity, thank you.

I meant search by similarity, thank you.
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