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Search: Posts Made By: liaoyunshi
Forum: Bioinformatics 01-20-2019, 06:33 PM
Replies: 7
Views: 1,537
Posted By liaoyunshi
Hi Martin, Sorry for leaving message in this...

Hi Martin,

Sorry for leaving message in this old post. But I find I meet similar situation with you and want to see if you have new idea after 2 years.

If my understanding is right, your...
Forum: Oxford Nanopore 01-18-2018, 12:13 AM
Replies: 4
Views: 3,055
Posted By liaoyunshi
I totally agree with you, I cannot imagine why we...

I totally agree with you, I cannot imagine why we should prepare 96 samples respectively in a way for a single sample library, and finally you need only 1/96 of each sample to be pooled.
Forum: Sample Prep / Library Generation 01-17-2018, 11:44 PM
Replies: 6
Views: 7,150
Posted By liaoyunshi
Hi, I also found it! Thanks. Actually...

Hi,

I also found it! Thanks.

Actually before reading this post, I just wondered why the second selection with less bead amount can capture small DNA. And I finally realize that it is the bead...
Forum: Oxford Nanopore 01-17-2018, 11:36 PM
Replies: 4
Views: 3,055
Posted By liaoyunshi
Hi Edinburgher, Quite happy to hear about...

Hi Edinburgher,

Quite happy to hear about people thinking the similar things as me, I even hope to change the reagent brand as the NEB is quite expensive.
Forum: Oxford Nanopore 01-17-2018, 05:01 PM
Replies: 4
Views: 3,055
Posted By liaoyunshi
Question Reducing use of NEB reagents in Nanopore barcoding (96) genomic DNA kit

Dear All,

Recently I used the nanopore 1D PCR barcoding (96) genomic DNA kit to construct the multiplex library. And I found that I need to use the standard volume of NEB reagent for the End prep...
Forum: Sample Prep / Library Generation 01-17-2018, 04:45 PM
Replies: 6
Views: 7,150
Posted By liaoyunshi
Hi nucacidhunter, So is that means the...

Hi nucacidhunter,

So is that means the factor deciding the DNA size capture is the bead solution volume instead of the bead amount itself?

Thanks.
Forum: Illumina/Solexa 01-10-2018, 01:37 AM
Replies: 1
Views: 961
Posted By liaoyunshi
how to self order illumina library and reagent

I am a new for Illumina, recently our lab want to prepare the illumina library by ourselves, without using the current kit. So I have the following questions would like to ask for your help.

1. Is...
Forum: Illumina/Solexa 01-10-2018, 01:20 AM
Replies: 14
Views: 3,374
Posted By liaoyunshi
Hi nucacidhunter, Yes I amplify large...

Hi nucacidhunter,

Yes I amplify large targets with few long overlapping amplicons and then to assemble it, but I need to do the fragmentation to make the size suitable for illumina sequencing. So...
Forum: Illumina/Solexa 01-09-2018, 06:26 PM
Replies: 14
Views: 3,374
Posted By liaoyunshi
Hi Seq_learner, nucacidhunter and Vasco, ...

Hi Seq_learner, nucacidhunter and Vasco,

Thanks for all your kindness. I do understand your protocol, but one bad news is that my DNA amplicons are much longer than several hundred bp, so I need...
Forum: Illumina/Solexa 01-08-2018, 09:20 PM
Replies: 3
Views: 938
Posted By liaoyunshi
Hi luc, I think the truseq-style barcodes...

Hi luc,

I think the truseq-style barcodes you mentioned is that kind of "multiplex index" within the adapter? The reason why we do not want to use such common way is that we want to conduct such...
Forum: Illumina/Solexa 01-08-2018, 06:01 PM
Replies: 3
Views: 938
Posted By liaoyunshi
How to add inline barcode to DNA fragment without PCR?

Dear all,

I want to use inline barcodes (barcode adjacent to the DNA fragment, included as the starting of the sequencing reads) for my illumina sequencing. Then I found most of current posts used...
Forum: Illumina/Solexa 01-08-2018, 05:06 PM
Replies: 14
Views: 3,374
Posted By liaoyunshi
Sorry to ask a naive question, may I know how to...

Sorry to ask a naive question, may I know how to add the inline barcodes adjacent to the sample DNA, through the specific design of PCR primer? I wonder if there is any kit can ligate the inline...
Forum: Bioinformatics 08-07-2017, 02:02 AM
Replies: 1
Views: 1,064
Posted By liaoyunshi
How to align multiple genomic regions simultaneously

Many thanks for reading my question.

Recently, I want to align multiple sequences from different genomic regions with the whole genome sequences for subsequent phylogenetic study, but I found none...
Forum: Bioinformatics 07-31-2017, 07:54 PM
Replies: 0
Views: 1,232
Posted By liaoyunshi
Question Question: canu correction process

Dear Fellows,

Recently, I started to use nanopore for sequencing, and use canu for the de novo assembly. After reading the manual and conduct some test run, I am curious about canu's correction...
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