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Search: Posts Made By: dickie_ho
Forum: Academic/Non-Profit Jobs 01-24-2018, 08:28 PM
Replies: 0
Views: 1,408
Posted By dickie_ho
Post-doctoral position in single cell sequencing in beautiful Newcastle, Australia

Hey seqanswers community

Dr Heather Lee is looking for a molecular or computational biologist. Great opportunity to work with a very talented researcher to progress your own career. To top it...
Forum: RNA Sequencing 08-29-2016, 06:28 PM
Replies: 0
Views: 1,749
Posted By dickie_ho
Open-source RNA-seq data for HEK293 cell lines ??

Hey all

Just trying to find some HEK293 RNA sequencing data for some of the new guys in our lab.. Would anyone know of a resource I could get either the sequencing data or to check what genes are...
Forum: Bioinformatics 07-04-2016, 06:04 AM
Replies: 2
Views: 802
Posted By dickie_ho
Thanks Bruce Will give that a shot, somehow...

Thanks Bruce

Will give that a shot, somehow I overlooked the intervals argument
Forum: Bioinformatics 07-04-2016, 04:13 AM
Replies: 2
Views: 802
Posted By dickie_ho
Is there a way to call variants from a BAM file based of a list of position ?

Hey all

Just trying to find a way to call around 100,000 single-point positions from BAM files calling both mismatches from the reference genome and also homozygous to the reference.

I can't...
Forum: Bioinformatics 07-04-2016, 04:04 AM
Replies: 1
Views: 726
Posted By dickie_ho
Hey mate Check this out...

Hey mate

Check this out https://github.com/lindenb/jvarkit/wiki/FixVcfMissingGenotypes

haven't used it yet myself, just regenerating all my bam files again because I ran into the same issue ...
Forum: Bioinformatics 06-30-2016, 03:54 AM
Replies: 1
Views: 4,005
Posted By dickie_ho
Hey mate First suggestion I would be using...

Hey mate

First suggestion I would be using plink 1.9 (don't have to worry about the annoying --noweb )

Try a process of elimination.. do a basic loop to to merge each chromosome separately...
Forum: Bioinformatics 02-12-2016, 01:42 AM
Replies: 4
Views: 1,334
Posted By dickie_ho
:(

Found out from the sequencing centre that its was the nano not the PCR-free kit ..... :(

Thank you for all your help Markiyan.. I would have spent a few more weeks trying to work this out if its...
Forum: Bioinformatics 02-08-2016, 04:04 PM
Replies: 4
Views: 1,334
Posted By dickie_ho
Hey Markiyan Thank you for your reply ...

Hey Markiyan

Thank you for your reply

The TruSeq PCR-free preps were used

Will check out the SNR.. thank you for this suggestion.. I will have a look and see if I can some how determine...
Forum: Bioinformatics 02-02-2016, 05:01 PM
Replies: 4
Views: 1,334
Posted By dickie_ho
CNVnator false positives -- Struggling

Hey everyone

I am having a hard time dealing with CNVnator .. well the results it generates..
I have array data, exome-seq data which the CNV calls line up .... Now using WGS data and I am...
Forum: General 10-22-2014, 02:38 AM
Replies: 9
Views: 1,943
Posted By dickie_ho
Thanks ulz_peter that is also a really good point...

Thanks ulz_peter that is also a really good point that i have managed to overlook

My set up at the moment is a 28TB linux box that i build for the purpose of WES and it does the job just fine...
Forum: General 10-21-2014, 05:55 PM
Replies: 9
Views: 1,943
Posted By dickie_ho
Cheers lh3

Cheers lh3
Forum: General 10-21-2014, 04:49 PM
Replies: 9
Views: 1,943
Posted By dickie_ho
Thanks dpryan This will help build my case...

Thanks dpryan

This will help build my case for WGS :)
Forum: General 10-21-2014, 01:37 AM
Replies: 9
Views: 1,943
Posted By dickie_ho
Thanks nucacidhunter Finding that missing...

Thanks nucacidhunter

Finding that missing heritability still remains the key especially in complex disease where the heterogeneity is that large, association is difficult.

I guess the big...
Forum: General 10-20-2014, 04:15 PM
Replies: 9
Views: 1,943
Posted By dickie_ho
Benefits of Whole genome sequencing over Exome sequencing

Hey everyone.

So what are the benefits from going from WES to WGS ???

Cheers for any help

Josh
Forum: General 04-26-2014, 01:42 PM
Replies: 0
Views: 2,164
Posted By dickie_ho
Any members at the HUGO 2014 ??

Hey everyone

So is anyone else going to HUGO 2014 in Geneva this week and has a cool poster i should check out ????

Cheers

Josh :)
Forum: Introductions 04-26-2014, 01:32 PM
Replies: 5
Views: 2,046
Posted By dickie_ho
lol sorry dude( i assume you are a guy) ... all i...

lol sorry dude( i assume you are a guy) ... all i can say is you have to learn it yourself.. no one/ or one tutorial is going to show you step by step ... mostly because it very complex and a crap...
Forum: Introductions 04-26-2014, 01:05 PM
Replies: 5
Views: 2,046
Posted By dickie_ho
The sky is the limit my friend ...... depends...

The sky is the limit my friend ...... depends what you would like to look at ... check out SnpEff
Forum: Introductions 04-16-2014, 03:54 AM
Replies: 3
Views: 1,438
Posted By dickie_ho
get some of the 1000 genome data and dick around...

get some of the 1000 genome data and dick around ........ everything you need to know is on the internet or on this forum :)
Forum: Bioinformatics 04-14-2014, 11:50 AM
Replies: 3
Views: 1,122
Posted By dickie_ho
Hey Meher Pros i would say having more data,...

Hey Meher
Pros i would say having more data, cons - different methods to get your data into penncnv (or your downstream pipeline).
It really depends on what type of analysis you want to do...
Forum: Bioinformatics 04-14-2014, 11:22 AM
Replies: 2
Views: 982
Posted By dickie_ho
mate check out the youtube videos on the GATK...

mate check out the youtube videos on the GATK package .. its not as simple as just using samtools to call out snps because INDELs and systematic biases affect the calls ... samtools does not adjust...
Forum: Bioinformatics 04-13-2014, 09:08 AM
Replies: 26
Views: 15,111
Posted By dickie_ho
Just to back Alberto EXCAVATOR is the best...

Just to back Alberto

EXCAVATOR is the best package i have came across for exome-seq data.

It has cross validated with my SNP array data and has even detected CNVs that the arrays did not...
Forum: Bioinformatics 04-13-2014, 09:01 AM
Replies: 1
Views: 1,430
Posted By dickie_ho
Hey Adrian I currently using excavator and...

Hey Adrian

I currently using excavator and I'm actually very impressed by it because it is the first program i have came across to have cross validation between my SNP array data and my...
Forum: Bioinformatics 02-17-2014, 02:50 PM
Replies: 3
Views: 1,495
Posted By dickie_ho
Smile Hey TiborNagy Do you suggest finding the...

Hey TiborNagy

Do you suggest finding the break points and lining that up with CNV information ??

Cheers

Josh
Forum: Bioinformatics 02-17-2014, 01:33 AM
Replies: 3
Views: 1,495
Posted By dickie_ho
Thanks TiborNagy Will have a good look...

Thanks TiborNagy

Will have a good look tomorrow ..
Forum: Bioinformatics 02-16-2014, 09:07 PM
Replies: 3
Views: 1,495
Posted By dickie_ho
Translocation detection using SNP arrays or exome-seq (no cell lines).. ideas ?

Hey seqanswers community

I am currently working on a CNV project using old data from illumina 610k arrays. I know this is almost impossible to detect translocation using a probe based method but...
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