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Forum: Academic/Non-Profit Jobs 06-30-2014, 08:26 AM
Replies: 1
Views: 1,680
Posted By silin284
RA Position in the Chinese University of Hong Kong

Research Associate Position in Bioinformatics
The School of Life Sciences, The Chinese University of Hong Kong

A research associate or research assistant position is available in the Zhong Lab,...
Forum: Sample Prep / Library Generation 02-27-2014, 09:28 PM
Replies: 1
Views: 3,326
Posted By silin284
home made EZ-Tn5-Nextera adapter complex?

Hi

Is it possible to mix equal molar of EZ-Tn5 transposase and the Nextera adapter to create a homebrew transposon?

It seems that the transposon in the Nextera kit contain 2 different adapter...
Forum: Illumina/Solexa 05-09-2013, 08:59 AM
Replies: 18
Views: 6,177
Posted By silin284
what is the "molecular indices" in the NEXTflex qRNA kit

Hi

I just saw the new NEXTflex RNA-Seq kit. They have this interesting "molecular indice" that would label each dsDNA molecule.
...
Forum: Sample Prep / Library Generation 01-26-2013, 08:41 AM
Replies: 5
Views: 2,629
Posted By silin284
contamination in DNA could cause that

I have seen that if the DNA has a lot of secondary metabolite. i work with plants so it is pretty common. you can clean up the dna using a column before ampure xp. we perfer to do a phenol chloroform...
Forum: Illumina/Solexa 01-15-2013, 10:58 AM
Replies: 31
Views: 16,702
Posted By silin284
Does anyone know the method of Moleculo's Long DNA Fragment Sequence?

Illumina's Moleculo Provides Long DNA Fragment Sequences to Improve Genomes, Clinical Assays

January 15, 2013

By Julia Karow

This article, originally published Jan. 14, has been updated with...
Forum: Illumina/Solexa 10-12-2011, 07:11 AM
Replies: 4
Views: 4,171
Posted By silin284
Hi Kmcarr and Heisman Thanks for the...

Hi Kmcarr and Heisman

Thanks for the replies. I can't blame the core for it too much, they have been stretched a lot recently. But I do need to find a way to sort the data...

With demultiplex,...
Forum: Illumina/Solexa 10-11-2011, 04:22 PM
Replies: 4
Views: 4,171
Posted By silin284
can user do the demultiplexing (truseq)

Hi

Our sequencing core is getting "tried" of demultiplexing the data for us since we put 20 homemade truseq index into each lane:(. They think it is a pain to send 7 x 20 fastq files to us each...
Forum: Sample Prep / Library Generation 08-27-2011, 07:46 AM
Replies: 12
Views: 7,404
Posted By silin284
for routine rna-seq, we include hexamers in the...

for routine rna-seq, we include hexamers in the fragmentation buffer to save some time, but for special libaries we have to add other oligos with hexamer in a later step like that protocol.
Forum: Sample Prep / Library Generation 08-20-2011, 01:42 PM
Replies: 12
Views: 7,404
Posted By silin284
superscript buffer can be used directly as fragmentation buffer

we have been using superscript3 buffer (2x) as fragmentation solution. After the one step fragmentation/elution, we add water, dntp etc to do the RT. Because the Superscript3 First-Strand buffer has...
Forum: Illumina/Solexa 05-12-2011, 08:16 PM
Replies: 7
Views: 8,318
Posted By silin284
if u use ligation buffer with ATP, u will...

if u use ligation buffer with ATP, u will circulate all ur small RNA rather than ligating them to 3SR linkers. Because sRNA, at least in plants, have 5' PO4 and 3'OH. I thought the 3' linker is a DNA...
Forum: Illumina/Solexa 05-12-2011, 08:07 PM
Replies: 3
Views: 3,286
Posted By silin284
clogged HiSeq, help needed

Hi

Our HiSeq2000 is experiencing a lot of fluidic problem recently. We will lose a lane or 2 during the run due to a clogged pump or maybe air bubble?. The Illumina engineer doesn't seem to have a...
Forum: Bioinformatics 12-05-2010, 05:54 PM
Replies: 313
Views: 109,006
Posted By silin284
support for poorly annotated genomes

Hi Simon

I do not have a EMBL style genome sequence. I only have the genome sequence file (fasta) and GTF file. Is there some tool to convert them into a format that SeqMonk can use?

Cheers
sz
Forum: Bioinformatics 12-05-2010, 05:46 PM
Replies: 313
Views: 109,006
Posted By silin284
support for poorly annotated genomes

Hi Simon

I do not have a EMBL style genome sequence. I only have the genome sequence file (fasta) and GTF file. Is there some tool to convert them into a format that SeqMonk can use?

Cheers
sz
Forum: Bioinformatics 12-03-2010, 10:53 AM
Replies: 3
Views: 4,302
Posted By silin284
Bug? duplicated genes in cufflinks output genes.expr

Hi

When i supplied a reference gtf to cufflinks (-G), i found there are duplicated geneID in the output "genes.expr". That is a bit weird to me and it is very rare (3 out of 50k genes). I checked...
Forum: Bioinformatics 12-03-2010, 10:40 AM
Replies: 15
Views: 7,644
Posted By silin284
thanks dariober, it seems the exon number is...

thanks dariober,

it seems the exon number is not a problem.

my GTF has genes in chromosome0 (unassembled stuffs) and the reference genome (bowtie index) does not. Removing the genes in...
Forum: Bioinformatics 11-30-2010, 08:43 PM
Replies: 15
Views: 7,644
Posted By silin284
tophat -G gene model annotations GTF format?

Hi

I use -G to supply a GTF file. But tophat show:

Warning: TopHat did not find any junctions in GTF file

I wonder what is wrong with my GTF file...

This is from my GTF file:
Forum: Bioinformatics 11-23-2010, 12:59 PM
Replies: 6
Views: 1,455
Posted By silin284
"bowtie --un filename.xxx" will save the unmapped...

"bowtie --un filename.xxx" will save the unmapped read to a specific file
Forum: Illumina/Solexa 11-12-2010, 01:26 PM
Replies: 0
Views: 2,108
Posted By silin284
Bridge amplification, Bst or Bst large fragment

Hi

Does Illumina use Bst or Bst Large fragment (which is 5->3 exo-) in the bridge amplification?

Can one replace this enzyme for just 1 lane to test?

Cheers
silin
Forum: Sample Prep / Library Generation 07-18-2010, 01:16 PM
Replies: 23
Views: 18,392
Posted By silin284
I have tried AMPure to clean up the ligation...

I have tried AMPure to clean up the ligation product and both 1.8 and 1.0 volume of AMPure beads work. I have never seen a 130 bp band after purification..... Is it possible that too much adapter...
Forum: Illumina/Solexa 05-01-2010, 06:59 AM
Replies: 16
Views: 17,173
Posted By silin284
Hi Xile 120 is the after PCR size. the SR...

Hi Xile

120 is the after PCR size. the SR pcr primers are 58 nt and 34. PE pcr primers are 58 and 61.

both SR and PE adapters are around 30 nt. So after ligation, only 60 bp were added to the...
Forum: Illumina/Solexa 04-30-2010, 06:57 AM
Replies: 16
Views: 17,173
Posted By silin284
I used the home made 100 mM ZnSO4 one. ...

I used the home made 100 mM ZnSO4 one.

However, I dont know why solexa recon cutting the 200 bp band. the RNA fragments are mainly 60-100 nt, the 2 adapters are around 60 in total. So the...
Forum: Illumina/Solexa 11-24-2009, 11:34 AM
Replies: 0
Views: 3,127
Posted By silin284
phosphorothioate and phusion

Hi

I would like to know more about the reason for having phosphorothioate bond in both the 3' end of the adapter and PCR primer.

In the case of the adapter: Is it correct that this can prevent...
Forum: Illumina/Solexa 10-23-2009, 05:34 PM
Replies: 24
Views: 27,712
Posted By silin284
Great idea. Some problem might come from the 30...

Great idea. Some problem might come from the 30 nt common linker.
1. It could generate bias to DNA with similar sequence (or a particular hairpin structure).
2. It also put a limit on the size of...
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