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Forum: RNA Sequencing 10-16-2019, 09:01 AM
Replies: 1
Views: 2,699
Posted By Vinn
Lexogen SENSE for de novo assembly?

Hi folks

I wonder if anyone would like to share experience with Lexogen SENSE for de novo assembly? I am considering using the kit as it can deal with much lower RNA input (some of my samples have...
Forum: Illumina/Solexa 10-18-2017, 07:20 AM
Replies: 10
Views: 4,248
Posted By Vinn
Hi Phillips, Do you have experience with...

Hi Phillips,

Do you have experience with 2-step PCR for Nextera XT V2 indexes? With the price of the XT indexing kit, we are looking for an alternative.

Illumina says base in adapter for N701...
Forum: Bioinformatics 04-26-2017, 01:56 PM
Replies: 8
Views: 2,704
Posted By Vinn
Thanks so much Brian for your advice. I will try...

Thanks so much Brian for your advice. I will try as you suggested. :)
Forum: Bioinformatics 04-25-2017, 06:48 AM
Replies: 8
Views: 2,704
Posted By Vinn
Thanks for your reply Brian. Just to be on a safe...

Thanks for your reply Brian. Just to be on a safe side, do you think it is better to trim the end off?
Forum: Bioinformatics 04-21-2017, 07:48 AM
Replies: 8
Views: 2,704
Posted By Vinn
Thank you, I will read the thread through. :)

Thank you, I will read the thread through. :)
Forum: Bioinformatics 04-21-2017, 07:17 AM
Replies: 8
Views: 2,704
Posted By Vinn
Hi GenoMax, thanks for your reply. I would like...

Hi GenoMax, thanks for your reply. I would like to do de novo assembly. :)
Forum: Bioinformatics 04-21-2017, 06:39 AM
Replies: 8
Views: 2,704
Posted By Vinn
K-mer content failed on 5' end - advice needed

Hi folks,

I am trying to do adapter and low quality trimming of a fungal genome (prepared with Illumina DNA nano kit and sequenced with HiSeq 2000 100PE). After using BBduk to trim adapters and...
Forum: Bioinformatics 04-11-2017, 02:36 AM
Replies: 9
Views: 2,249
Posted By Vinn
Hi Brian, Thank you very much; I will try...

Hi Brian,

Thank you very much; I will try as you suggested. :) Anyway, I couldn't stop wondering what if I trim both R1 and R2 reads to 150 bp using bbduk (ftr=150), and use them as a 150PE?
Forum: Bioinformatics 04-10-2017, 12:17 PM
Replies: 9
Views: 2,249
Posted By Vinn
Dear Brian, Thanks for your reply and for...

Dear Brian,

Thanks for your reply and for the suggestion. I will try merging and reassembling again.
Happy Easter holiday! :)
Forum: Bioinformatics 04-10-2017, 12:12 PM
Replies: 9
Views: 2,249
Posted By Vinn
Dear Ola, Thanks for your reply and for...

Dear Ola,

Thanks for your reply and for your suggestion. I just received another library with another insert size and will try using it to improve the one I have. :)

Have a great Easter...
Forum: Bioinformatics 04-10-2017, 12:06 PM
Replies: 9
Views: 2,249
Posted By Vinn
Dear Genomax, Thanks for your reply and for...

Dear Genomax,

Thanks for your reply and for the suggestion. I was thinking about that too, but since I just got another PE library (with another insert size), I am not sure if SPAdes can handle...
Forum: Bioinformatics 04-09-2017, 03:07 PM
Replies: 9
Views: 2,249
Posted By Vinn
Please help with assembly 2x250 bp with 350 insert

Hi folks,

I have got data generated from 2x250 bp with 350 bp insert for fungal genome assembly. I got very good results from SPAdes, but later discovered that SPAdes recommends an insert of...
Forum: Illumina/Solexa 09-21-2016, 12:22 PM
Replies: 2
Views: 998
Posted By Vinn
Truseq 5' adapters

Hi folks

I am a newbie trying to trim adapters from my fungal genome data. It is generated with TruSeq PCR-free 350 bp insert/Hiseq 2500 (250 PE). I read manuals of some trimmers and it seems they...
Forum: Sample Prep / Library Generation 08-21-2016, 10:26 AM
Replies: 1
Views: 1,189
Posted By Vinn
Please help! DNA samples for whole genome sequencing

Hi folks,

I have extracted DNA from fungi for whole genome sequencing (Truseq PCR free with 350 bp insert and HiSeq 2500 PE) using a kit. The extraction went smooth until I realized at the end...
Forum: RNA Sequencing 07-11-2016, 04:03 AM
Replies: 0
Views: 957
Posted By Vinn
Trinity assembly and qPCR

Hi folks,

I have new RNAseq data assembled with Trinity, and now I am trying to use qPCR for validation. I blasted a gene of interest from another species against the RNAseq data for primer...
Forum: Illumina/Solexa 04-12-2016, 08:14 AM
Replies: 5
Views: 2,106
Posted By Vinn
Hi folks Thank you again for all great and...

Hi folks

Thank you again for all great and useful advice. Just a small question, do you think in my case it is possible to get a good assembly with only a 550bp paired-end library? Or it comes...
Forum: Illumina/Solexa 04-11-2016, 07:17 PM
Replies: 5
Views: 2,106
Posted By Vinn
sequencing paired-end and mate-pair libraries in a single lane?

Hi folks,

We are new to genome sequencing, but we want to sequence fungal genomes using Hiseq. We were wondering if it is possible to include both mate-pair (2 or 3 kb) and paired-end (either 300...
Forum: Sample Prep / Library Generation 02-09-2015, 08:56 AM
Replies: 0
Views: 981
Posted By Vinn
DNA extraction for amplicon sequencing

Hi folks,

Sorry for having a very basic question here. I am going to use amplicon sequencing to study endophytes in tree. I was wondering whether it is necessary to perform DNA extraction under...
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