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Search: Posts Made By: usad
Forum: Introductions 12-22-2016, 09:59 AM
Replies: 5
Views: 2,680
Posted By usad
oxford now

Oxford nanopores changed dramatically in output a couple of months ago. Have a look at the data prereleases. 2-7 Gbases per run was normal for us (with a bit of experience)
Error rate is of course...
Forum: Introductions 07-05-2016, 03:18 AM
Replies: 2
Views: 861
Posted By usad
Hi David welcome and no worries, it will not...

Hi David

welcome and no worries, it will not be too difficult. (The main problem will be to get the unpublished lettuce genome data and making sure you can use it).

Best Wishes
Björn
Forum: Bioinformatics 09-13-2015, 07:10 AM
Replies: 6
Views: 1,260
Posted By usad
you can also just run trimmomatic without the...

you can also just run trimmomatic without the phred switch and it will try to autodetect quality scores (since 0.32)

Best Wishes
björn
Forum: Bioinformatics 05-18-2015, 03:30 AM
Replies: 5
Views: 5,207
Posted By usad
Hi Nicolas the keeppaired is more a comfort...

Hi Nicolas

the keeppaired is more a comfort option, so you still have paired reads. You will not loose reads by not using it, but they might end up in a different "bin" (i.e.file).

e.g. ...
Forum: Bioinformatics 12-12-2014, 09:01 AM
Replies: 6
Views: 2,706
Posted By usad
Was the overrepresented sequence nuclear encoded?...

Was the overrepresented sequence nuclear encoded?
And did you do polyA enriched RNA and are wondering about the lack of plastome encoded gene expression?

As polyadenylation has a very different...
Forum: Academic/Non-Profit Jobs 09-11-2014, 11:20 PM
Replies: 0
Views: 562
Posted By usad
Two Positions at Research Center Juelich

Dear SeqAnswers Members

at the moment we have two positions availble:

1)
A postdoctoral position

The ideal candidate will have a strong computing background combined with experience working...
Forum: Bioinformatics 09-02-2014, 06:56 AM
Replies: 52
Views: 20,719
Posted By usad
The ^M would indicate you have a windows file on...

The ^M would indicate you have a windows file on a linux system.
Try dos2unix on the script and try again.
Forum: Bioinformatics 06-17-2014, 07:51 AM
Replies: 189
Views: 66,668
Posted By usad
great that it works now.

great that it works now.
Forum: Bioinformatics 06-15-2014, 01:30 PM
Replies: 189
Views: 66,668
Posted By usad
Hi sorry for the inconvenience. At the...

Hi

sorry for the inconvenience. At the moment it might be best to not have to use C: at all as trimmomatic looks for data after :
E.g. having the clip file in the actual directory - yukk.

Best...
Forum: Illumina/Solexa 05-29-2014, 12:34 AM
Replies: 6
Views: 2,463
Posted By usad
Hi Elsie if you have your own Miseq, you can...

Hi Elsie

if you have your own Miseq, you can also get slightly longer runs. (We picked his up from here) but this is totally unsupoorted though.

björn
Forum: Illumina/Solexa 05-27-2014, 11:09 PM
Replies: 6
Views: 2,463
Posted By usad
Hi it might also be advisable to check...

Hi

it might also be advisable to check (consider) the homozygosity. (If you have some coverage you see this in kmer plots). But you can also estimazte this if this is an inbred line and whether or...
Forum: Bioinformatics 01-10-2014, 12:21 PM
Replies: 1
Views: 2,047
Posted By usad
Hi Acrolombo Trimmomatic will (in this...

Hi Acrolombo

Trimmomatic will (in this paired case) generated four files from your set of two files (FW & RV)
First a new pair of FW and RV reads which are still paired. This is indicated by...
Forum: Bioinformatics 01-09-2014, 08:54 AM
Replies: 13
Views: 2,735
Posted By usad
Ah ok I see, yeah different names for the same...

Ah ok I see, yeah different names for the same thing is a major bummer. But instead of having a data warehouse concept, maybe you could relalize the same thing by using some AJAXian data collector...
Forum: Bioinformatics 01-08-2014, 07:01 PM
Replies: 13
Views: 2,735
Posted By usad
Hi so if I understand it correctly a) a gene...

Hi
so if I understand it correctly a) a gene annotation pipeline and b) a compedium of well evaluated data?

a) I would be careful beause annotation is not annotation (you might want to go deeply...
Forum: RNA Sequencing 12-04-2013, 10:23 AM
Replies: 5
Views: 2,157
Posted By usad
Hi, This is of course difficult to say. ...

Hi,

This is of course difficult to say.
Also with your BLAST searches. But if you re-assemble a genome from scratch with stringent adapter removal and the adapters dissappear it is a good...
Forum: Bioinformatics 11-28-2013, 02:22 AM
Replies: 3
Views: 3,282
Posted By usad
Hi yes it does (and bz2 as well), no need to...

Hi

yes it does (and bz2 as well), no need to unzip the fastq files.

Best Wishes
Björn
Forum: Bioinformatics 11-28-2013, 02:20 AM
Replies: 7
Views: 3,340
Posted By usad
Hi sliding window will only remove bad quality...

Hi
sliding window will only remove bad quality bases. To remove adapters you should [also] use Illuminaclip.

best
bjrön
Forum: General 10-01-2013, 03:40 AM
Replies: 6
Views: 3,189
Posted By usad
the ngs field guide: ...

the ngs field guide:
http://www.molecularecologist.com/next-gen-fieldguide-2013/
I like it as it is updated every year. (so far)
Forum: Bioinformatics 09-09-2013, 03:37 AM
Replies: 3
Views: 2,923
Posted By usad
Hi JDBelgium I reckon when you say de-novo...

Hi JDBelgium

I reckon when you say de-novo you mean from sequence=>assembly=>DE genes?
We considered this for RobiNA but at the moment transcriptome assemblies are still quite "heavy".

Best...
Forum: RNA Sequencing 08-22-2013, 01:33 PM
Replies: 5
Views: 2,157
Posted By usad
Hi Veronica adapters might "become" part of...

Hi Veronica

adapters might "become" part of your genome (you see this in a few draft genomes) or cause bridges.

You could try searching your genomes against all the possible adapter/primer...
Forum: Bioinformatics 08-01-2013, 06:03 AM
Replies: 30
Views: 6,111
Posted By usad
Hi Dan I was logged in (this works...

Hi Dan

I was logged in (this works flawlessly I never get logged out- thanks god) But maybe I don't have Wikipedia credibility yet.

I will simpley omit the references. Most are in anyway.
...
Forum: Bioinformatics 07-23-2013, 07:18 AM
Replies: 30
Views: 6,111
Posted By usad
Hi Dan considering how much work (unsolvable...

Hi Dan

considering how much work (unsolvable CAPTCHAS) it is to put a reference it Wikipedia, maybe it is really worth considering to move this to the trusted SeqanswersWIKI site?

Best Wishes,...
Forum: Bioinformatics 07-22-2013, 01:01 PM
Replies: 30
Views: 6,111
Posted By usad
on it now I have added different metrics for...

on it now
I have added different metrics for the completeness, maybe it is worthwile to split them up columnwise. well see for yourself
(apple/papaya/cucumber)

next corn/ricinus/solanace/peach
...
Forum: Bioinformatics 07-11-2013, 12:14 AM
Replies: 30
Views: 6,111
Posted By usad
Thanks, sure I will go ahead.

Thanks, sure I will go ahead.
Forum: Bioinformatics 07-10-2013, 03:39 AM
Replies: 30
Views: 6,111
Posted By usad
Hi Dan et al I can likely help as well, but...

Hi Dan et al

I can likely help as well, but a couple things:
The classification definitely makes sense, but I reckon it would also be helpful to have everything in one table so it can be copied...
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