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Forum: Bioinformatics 10-24-2019, 06:53 AM
Replies: 1
Views: 1,020
Posted By wingtec
analyze kallisto rnaseq data

Hi All,

I wonder how people analyze Kallisto data (estimated counts), using any bioconductor packages?

Thanks

Wingtec
Forum: General 10-21-2016, 05:29 AM
Replies: 1
Views: 1,672
Posted By wingtec
genomeNext

Hi Forum,

I wonder if anyone has experience using the fee-based bioinformatics services from a company called GeonomeNext, or care to share any comments on it.

Best,

Wing
Forum: General 04-29-2016, 11:23 AM
Replies: 0
Views: 1,182
Posted By wingtec
tophat error -- image not found

Hi All,

Can someone help for this --

While running TopHat 2.1.1 OS X I repeatedly ran into this error:

Searching for junctions via segment mapping
Coverage-search algorithm is turned on,...
Forum: General 04-19-2016, 10:23 AM
Replies: 5
Views: 2,079
Posted By wingtec
I am just wondering if I can take a piggy-back of...

I am just wondering if I can take a piggy-back of the APPs in BaseSpace for analysis of, say, RNA-Seq data, which were generated outside of BaseSpace.

Thanks

W
Forum: General 04-14-2016, 06:10 AM
Replies: 5
Views: 2,079
Posted By wingtec
use of BaseSpace app for outside data

Hi All,

Has anyone tried to import outside work into a project in BaseSpace and then use the Apps in BaseSpace to process the data, such as tophat?

Thanks

Wing
Forum: General 07-28-2015, 06:11 AM
Replies: 0
Views: 1,131
Posted By wingtec
Novogene corporation Inc.

Hi All,

I wonder if anyone has experiences doing business with Novogene, an international company based in China-Hong Kong, in terms of the deep sequencing services they provide. Any comments will...
Forum: Illumina/Solexa 02-05-2015, 05:41 AM
Replies: 8
Views: 3,499
Posted By wingtec
With all that said, if I am allowed to twist the...

With all that said, if I am allowed to twist the question a bit.

Say, I already have some Affy microarray data and I want to better or at least confirm the array data with RNA-Seq. The Affy chip...
Forum: Illumina/Solexa 02-04-2015, 06:49 PM
Replies: 8
Views: 3,499
Posted By wingtec
Thanks much to y'all. These are very useful as...

Thanks much to y'all. These are very useful as well as practical helps!

Wing
Forum: Illumina/Solexa 02-04-2015, 09:27 AM
Replies: 8
Views: 3,499
Posted By wingtec
How many million reads required to have a 20x coverage for rat RNA

Hi All,

Try to seek a piece of advice --- we are trying to obtain an average coverage of 20x for RNA-Seq of rat tissues. How many million reads should we try to get for each library to have that...
Forum: General 10-30-2014, 10:55 AM
Replies: 2
Views: 1,550
Posted By wingtec
Thanks, CMBETT. For me a bigger concern is...

Thanks, CMBETT.

For me a bigger concern is wether this will mess up the denaturation step, especially in the case where the ExoSap reaction does not get high enough dilution based on...
Forum: General 10-29-2014, 06:01 AM
Replies: 2
Views: 1,550
Posted By wingtec
ExoSap purified PCR product compatible for Illumina sequencing?

Hi All,

Does anyone have experience with purification of PCR amplicons using ExoSap Endonuclease treatment? I wonder if this procedure is compatible with MiSeq sequencing.

Best,

Wing
Forum: Illumina/Solexa 05-23-2014, 08:18 AM
Replies: 0
Views: 1,024
Posted By wingtec
support files for small RNA-Seq for mouse

Hello,

Dose anyone have those files for mouse small RNA-Seq as required in the Illumina Experiment Manager -- Contaminant, RNA, and miRNA? I understand that for human you can download those files...
Forum: Illumina/Solexa 05-07-2014, 07:05 AM
Replies: 2
Views: 1,855
Posted By wingtec
Thank you for your answer, NUACIDHUnTER! This is...

Thank you for your answer, NUACIDHUnTER! This is assuring.

Wingtec
Forum: Illumina/Solexa 05-05-2014, 08:16 AM
Replies: 2
Views: 1,855
Posted By wingtec
how many cycles to run for truseq small RNA libraries

Hi All,

I wonder how many cycles others choose to run for TruSeq small libraries and if they will select the option of trimming the adaptor sequences.

Thanks

Wingtec
Forum: Ion Torrent 12-15-2013, 06:32 AM
Replies: 12
Views: 9,932
Posted By wingtec
Hi Muthu et al., Thanks much for the quick...

Hi Muthu et al.,

Thanks much for the quick reply for picking up my stupid omission of a main switch. After the fix, I am happy to report that everything works beautifully.

Wing
Forum: Ion Torrent 12-13-2013, 11:49 AM
Replies: 12
Views: 9,932
Posted By wingtec
subset fastq according to sequence lengths

Hi,

Thanks for your Python script.

However, when I was trying to run it in my Mac (OSX) I got the following error message:

d-128-54-196:PythonApps yb8d$ python...
Forum: Bioinformatics 10-16-2013, 08:01 AM
Replies: 0
Views: 771
Posted By wingtec
bwa trouble making index

Hi,

While I was trying to make index for bwa, I encountered this error:


d-128-61-165:bwa-0.7.5a xxx$ ./bwa index -p EMCTargetbwaidx -a bwtsw EntamoebaCTarget.fa
[bwa_index] Pack FASTA......
Forum: Bioinformatics 09-30-2013, 07:29 AM
Replies: 1
Views: 5,498
Posted By wingtec
wigtobigwig

Hi,

Can someone tell me if there is a version of wigToBigwig for Mac OSX? All I can find is the version for Linux 64bit.

Thanks

Wing
Forum: Bioinformatics 09-04-2013, 09:53 AM
Replies: 2
Views: 9,919
Posted By wingtec
Thanks so much. So this is the thing I forgot. ...

Thanks so much. So this is the thing I forgot.

Wing
Forum: Bioinformatics 09-03-2013, 11:33 AM
Replies: 2
Views: 9,919
Posted By wingtec
UCSC bedGraphToBigWig executable?

hello,

I was trying to make use of some the stand-alone packages in UCSC download:
such as http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/

But I do not know how to make the downloaded...
Forum: General 07-07-2013, 03:44 PM
Replies: 0
Views: 1,248
Posted By wingtec
illumina truseq chip-seq library

Hi All,

Has anyone tried to make genomic library with the Illumina TruSeq ChIP-Seq library kits? If so, how did it work?

Best,

Wingtec
Forum: Illumina/Solexa 01-31-2013, 12:43 PM
Replies: 0
Views: 2,837
Posted By wingtec
Nextera primers

Hi All,

In its customer sequence letter (5/20/2012) Illumina did reveal some primer sequences used in various kinds of application. But it is not clear as what they really are for such as Nextera...
Forum: Illumina/Solexa 01-25-2013, 05:47 AM
Replies: 0
Views: 1,836
Posted By wingtec
TruSeq Custom Amplicon

Hi All,

I wonder if anyone can point me to a publication using Illumina TruSeq Custom Amplicon, with kind of in-depth description of the method and designs. My own search did not come up anything...
Forum: General 09-28-2012, 12:17 PM
Replies: 3
Views: 1,770
Posted By wingtec
Terrific! Thanks so much. Wingtec

Terrific! Thanks so much.

Wingtec
Forum: General 09-28-2012, 11:01 AM
Replies: 3
Views: 1,770
Posted By wingtec
shopping around to outsourcing genomic sequencing

Hi All,

I remember seeing a list of commercial or academic institutes offering deep sequencing service, a while back in this forum. Can someone in the know point me to find it?

Many thanks
...
Showing results 1 to 25 of 34

 


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