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Search: Posts Made By: marcowanger
Forum: Bioinformatics 06-28-2016, 05:08 PM
Replies: 1
Views: 664
Posted By marcowanger
Hi Jason, Thanks for your interest in using...

Hi Jason,

Thanks for your interest in using ViralFusionSeq and I apologize that you could not run stock VFS against a whole virus database.

I am currently occupied in other projects so I could...
Forum: Bioinformatics 01-16-2014, 06:14 PM
Replies: 13
Views: 2,112
Posted By marcowanger
Dear IBseq, First you need to run...

Dear IBseq,

First you need to run 1.VFS.sys.check.pl to see if the dependencies can be called successfully. If you have already done that, then it is nice.

Then you either run viral.fusion.pl...
Forum: Bioinformatics 01-05-2014, 11:44 PM
Replies: 3
Views: 1,485
Posted By marcowanger
Hi akhattri and dietmar13, I suppose there was...

Hi akhattri and dietmar13, I suppose there was some problem in processing the gzipped fastq files (that subsequently lead to the problem you see), I should have fixed the problem.

Would you mind...
Forum: Bioinformatics 01-05-2014, 08:11 PM
Replies: 13
Views: 2,112
Posted By marcowanger
akhattri, I am looking at your problem now.:)

akhattri, I am looking at your problem now.:)
Forum: Bioinformatics 07-30-2013, 09:52 AM
Replies: 13
Views: 2,112
Posted By marcowanger
Hi eli, did the single thread version of VFS...

Hi eli, did the single thread version of VFS works?
Forum: Bioinformatics 07-18-2013, 02:20 AM
Replies: 13
Views: 2,112
Posted By marcowanger
Hi eligar97, Which version fo VFS did you...

Hi eligar97,

Which version fo VFS did you download?

Are you running VFS on Ubuntu system, or others?

Marco
Forum: General 04-16-2013, 09:02 PM
Replies: 8
Views: 98,530
Posted By marcowanger
Joann, It would be good if we can do so! ...

Joann,

It would be good if we can do so!

AdaptiveGenome,

I think the GCAT would be very useful, not only on evaluating pipelines in a more interactive way. At certain time point, would you...
Forum: Bioinformatics 03-07-2013, 12:41 AM
Replies: 11
Views: 1,660
Posted By marcowanger
I think all make sense.

I think all make sense.
Forum: Bioinformatics 01-29-2013, 09:43 PM
Replies: 11
Views: 1,660
Posted By marcowanger
I think that is why we need a database for this...

I think that is why we need a database for this ..:)
Forum: Bioinformatics 01-29-2013, 07:18 AM
Replies: 11
Views: 1,660
Posted By marcowanger
i think multiple values may be better. If only 1...

i think multiple values may be better. If only 1 single value is allowed, it might becomes a reference price list by manufacturer (IMHO, is useless and miss the point of community oriented).
Forum: Bioinformatics 01-29-2013, 06:20 AM
Replies: 11
Views: 1,660
Posted By marcowanger
Another thought is, machine and reagent...

Another thought is,

machine and reagent costs vary from country to country. I think it depends who you are (big institution or small, etc). And throughput depends on how much you can squeeze out.....
Forum: Bioinformatics 01-29-2013, 06:16 AM
Replies: 11
Views: 1,660
Posted By marcowanger
Hi Dan, You make me think of this...

Hi Dan,

You make me think of this http://www.molecularecologist.com/next-gen-fieldguide-2012/
Forum: Bioinformatics 01-18-2013, 09:15 AM
Replies: 18
Views: 2,103
Posted By marcowanger
You may want to try VirusSeq or VirusFusionSeq ...

You may want to try VirusSeq or VirusFusionSeq

http://seqanswers.com/wiki/VirusSeq
http://seqanswers.com/wiki/ViralFusionSeq
Forum: Bioinformatics 01-14-2013, 04:50 AM
Replies: 2
Views: 1,049
Posted By marcowanger
I remember Bam2fastq only export read pair. So,...

I remember Bam2fastq only export read pair. So, all singleton mapped will be discarded. In your case, it may be better to write a small script to parse the singleton out
Forum: Literature Watch 01-13-2013, 11:13 PM
Replies: 0
Views: 1,147
Posted By marcowanger
Thumbs up ViralFusionSeq

ViralFusionSeq: Accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution:)

Summary: Insertional mutagenesis from virus infection is an important...
Forum: Introductions 11-29-2012, 07:14 PM
Replies: 2
Views: 814
Posted By marcowanger
Greeting from Hong Kong. Good to know you...

Greeting from Hong Kong.

Good to know you Sunny.
Forum: General 11-24-2012, 01:28 AM
Replies: 8
Views: 98,530
Posted By marcowanger
Thanks Joann

Thanks Joann
Forum: General 11-22-2012, 10:57 PM
Replies: 8
Views: 98,530
Posted By marcowanger
One question, I am not sure about the Minimum...

One question, I am not sure about the Minimum information about array. How was that minimal information about microarray expression got accepted as the standard for publication? What was the turning...
Forum: Bioinformatics 11-21-2012, 07:41 AM
Replies: 2
Views: 1,250
Posted By marcowanger
The short answer: nope

The short answer: nope
Forum: Sample Prep / Library Generation 11-20-2012, 07:25 PM
Replies: 3
Views: 1,359
Posted By marcowanger
For general idea:...

For general idea: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_(NGS)
Forum: General 11-13-2012, 07:22 PM
Replies: 8
Views: 98,530
Posted By marcowanger
The SEQwiki page:...

The SEQwiki page: http://seqanswers.com/wiki/Standard

The MINSEQE page by FGED: http://www.mged.org/minseqe/
Forum: Illumina/Solexa 10-12-2012, 02:05 AM
Replies: 6
Views: 3,149
Posted By marcowanger
deadline is coming, figuredsomething out?

deadline is coming, figuredsomething out?
Forum: Service Providers 09-25-2012, 07:48 AM
Replies: 22
Views: 22,602
Posted By marcowanger
not good for everyone ...

not good for everyone ...
Forum: Service Providers 09-25-2012, 07:48 AM
Replies: 22
Views: 22,602
Posted By marcowanger
lh3, your description is so concise :)

lh3, your description is so concise :)
Forum: Bioinformatics 09-24-2012, 08:19 AM
Replies: 7
Views: 2,068
Posted By marcowanger
Hi Allen, Yes, you need to sort your Fastq...

Hi Allen,

Yes, you need to sort your Fastq input before running Novoalign. No luck man.
Showing results 1 to 25 of 352

 


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