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Forum: Sample Prep / Library Generation 05-02-2017, 05:50 AM
Replies: 2
Views: 1,591
Posted By Dampor
ATAC-seq plasmid contamination after transfection

HI all

I am trying to produce ATAC-seq libraries from transfected cells, but it seems a pain...

I have produced good libraries from non-transfected cells (sequencing was OK), but when I...
Forum: Sample Prep / Library Generation 02-23-2017, 03:26 AM
Replies: 2
Views: 2,606
Posted By Dampor
Hi, did you get any feedback on those...

Hi,
did you get any feedback on those libraries?
I have got something similar but from different cells.
Did you sequenced them at the end? if yes, how was the result?

Thanks
Dam
Forum: Bioinformatics 02-23-2015, 05:17 AM
Replies: 7
Views: 4,015
Posted By Dampor
Thanks Frank! Although I have almost done...

Thanks Frank!

Although I have almost done with the analyses now, I'll have a look and keep in mind for the future

Cheers
D
Forum: Bioinformatics 11-25-2014, 02:43 PM
Replies: 1
Views: 1,621
Posted By Dampor
Arrow Question for experts in normalization

Hi Guys

I have replicated RNA-seq samples from 6 populations at 2 different treatments (benign and heat stress) repeated at two separate times (year 1 and year 2).
I am looking for the best way...
Forum: Bioinformatics 08-04-2014, 05:23 AM
Replies: 7
Views: 4,015
Posted By Dampor
Tanks for the reply colindaven, (forgot to...

Tanks for the reply colindaven,

(forgot to mention) unfortunately there is no reference genome... therefore I need to get the transcriptome annotated as accurate as possible for the pop gen...
Forum: Bioinformatics 08-04-2014, 04:50 AM
Replies: 7
Views: 4,015
Posted By Dampor
Big question - Transcriptome annotation

Hi guys,

I have just finished to assemble my transcriptome ( I used Trinity, N50 is 2000, I am quite happy with it).
Now I would like to annotate it, particularly for doing some SNPs calling and...
Forum: Bioinformatics 01-14-2014, 01:34 AM
Replies: 2
Views: 1,246
Posted By Dampor
Hi TiborNagy, thanks for your reply... Can you...

Hi TiborNagy, thanks for your reply...
Can you please tell me how efficient is this method?
What the percentage-ish of resolution of the "multigene" contigs?
Cheers
Forum: Bioinformatics 01-13-2014, 01:52 AM
Replies: 2
Views: 1,246
Posted By Dampor
de novo transcriptome Trinity Assembly concatenamers

Hi all,

I got a de novo transcriptome Trinity assembly of a drosophila species which is evolutionary far from other sequenced species (closest one is pseudoobscura, but 10% divergency at least)....
Forum: Bioinformatics 09-24-2013, 08:03 AM
Replies: 15
Views: 8,915
Posted By Dampor
Thank you guys, I did actually decide to try...

Thank you guys,

I did actually decide to try both approaches :)
My result will follow in this thread.

@westerman, also, what tool will allow me to combine data sets using protein translations?...
Forum: Bioinformatics 09-09-2013, 12:14 AM
Replies: 15
Views: 8,915
Posted By Dampor
Hi Jeremy Unfortunately there is not a...

Hi Jeremy

Unfortunately there is not a sequenced genome for this species yet
The closest sequenced genome is D. pseudoobscura, which is already 9% divergent (just at coding sequences).
Thanks....
Forum: Bioinformatics 09-06-2013, 05:51 AM
Replies: 15
Views: 8,915
Posted By Dampor
Thank guys! Last comment from rskr concerns me...

Thank guys!
Last comment from rskr concerns me actually.

wouldn't be better if I can combine transcripts from the two pools by matching their translation, so use protein sequences?
What tools...
Forum: Bioinformatics 09-05-2013, 07:06 AM
Replies: 15
Views: 8,915
Posted By Dampor
merge two Trinity transcriptome assemblies into one

Hi All

I have got two transcriptomes from two populations of a Drosophila species, both assembled using Trinity.
How can I merge those into one final comprehensive transcriptome?
Please note...
Forum: Sample Prep / Library Generation 04-12-2013, 01:03 AM
Replies: 0
Views: 1,555
Posted By Dampor
trizol + RNeasy tot RNA extractions: decrease trend in last samples concentration

Hi there

I have done several (about 800) tot RNA extractions using trizol followed by RNeasy clean-up.
I usually do 20 samples per day. Although I am generally satisfied with what I get,...
Forum: Illumina/Solexa 03-01-2013, 08:42 AM
Replies: 1
Views: 1,366
Posted By Dampor
BGI illumina RNA-seq comparison

Hi there

I want to ask if someone compared data from BGI Illumina 50bp single end RNA-seq, where they use an optimized Illumina protocol for libraries preparation, with same kind of data (samples)...
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