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Search: Posts Made By: zhaopeihua
Forum: Bioinformatics 08-25-2014, 05:59 PM
Replies: 6
Views: 3,071
Posted By zhaopeihua
Just need an indicator reflects genome similarity

Just need an indicator reflects genome similarity
Forum: Bioinformatics 08-25-2014, 05:49 PM
Replies: 6
Views: 3,071
Posted By zhaopeihua
I wanna use the proportion of animal genome that...

I wanna use the proportion of animal genome that could be align to human representing similarity, is this way reasonable?
Forum: Bioinformatics 08-24-2014, 10:02 PM
Replies: 6
Views: 3,071
Posted By zhaopeihua
how to measure similarity between species genome?

hi,

How to calculate similarity between humans and animals?
For example, Chimpanzees are 96% genetically similar to humans.
Forum: Bioinformatics 04-03-2014, 04:10 AM
Replies: 4
Views: 1,982
Posted By zhaopeihua
What is the meaning of fold expression?

What is the meaning of fold expression?
Forum: Bioinformatics 04-03-2014, 12:56 AM
Replies: 4
Views: 1,982
Posted By zhaopeihua
how to normalize RNA-seq with microarray data?

hi,

I have some gene expression data measured by RNA-seq or microarray. but RNA-seq data gene expression level generally higher than microarray.How should I normalize the data to find the...
Forum: Bioinformatics 03-24-2014, 11:37 PM
Replies: 2
Views: 2,026
Posted By zhaopeihua
TCGA mRNA data

hi,

I have downloaded some cancer level3 mRNA data from TCGA. Are there matched-normal tissue samples in data set ? or just cancer sample ?
Forum: Metagenomics 01-26-2014, 01:01 AM
Replies: 1
Views: 2,472
Posted By zhaopeihua
the weighted UniFrac distances are bigger than one is normal ?

hi,

I use the following Qiime command to calculate weighted/unweighted UniFrac distances. the unweighted UniFrac distances are all between 0 and 1.but some weighted UniFrac distances are >1....
Forum: Metagenomics 11-27-2013, 05:57 PM
Replies: 7
Views: 8,930
Posted By zhaopeihua
How to install qiime?

hi,

I am trying to install qiime-deploy using follow command:

"python qiime-deploy.py $HOME/qiime_software/ -f $HOME/qiime-deploy-conf/qiime-1.7.0/qiime.conf --force-remove-failed-dirs"
...
Forum: Bioinformatics 11-23-2013, 01:44 AM
Replies: 5
Views: 7,134
Posted By zhaopeihua
how to annotate somatic mutation?

hi:
I have map the tumor-normal pair exome data to genome using BWA and calling somatic mutation using Varcan. how to annotate somatic mutaion? just like classify the somatic mutation to ...
Forum: Bioinformatics 11-19-2013, 12:40 AM
Replies: 1
Views: 1,362
Posted By zhaopeihua
how to download data from “The European Genome-phenome Archive”?

hi:
I need some data from The European Genome-phenome Archive,but the dataset requires access control,how could i get it?
thanks in advance!
Forum: Metagenomics 10-31-2013, 04:25 AM
Replies: 8
Views: 15,107
Posted By zhaopeihua
thanks for your reply I hava checked this...

thanks for your reply

I hava checked this tutorial, it used for single-end,but I want to process pair-end data.
Do you know other tutorial or approach to do this? thank again.
Forum: Metagenomics 10-28-2013, 03:18 AM
Replies: 8
Views: 15,107
Posted By zhaopeihua
How to use QIIME process MiSeq 16s data?

Hi:

I’m totally new to this area, I've got some MiSeq 16S data. Is there tutorial like 454 Overview Tutorial("http://qiime.org/tutorials/tutorial.html") on QIIME website?

thanks in...
Forum: Bioinformatics 10-24-2013, 12:12 AM
Replies: 10
Views: 20,178
Posted By zhaopeihua
Awesome, thanks!

Awesome, thanks!
Forum: Bioinformatics 10-23-2013, 10:13 PM
Replies: 10
Views: 20,178
Posted By zhaopeihua
thanks for you reply,but I didn't fully...

thanks for you reply,but I didn't fully understand this concept. Could you show me a detail example with computational process? thanks again
Forum: Bioinformatics 10-23-2013, 02:54 AM
Replies: 10
Views: 20,178
Posted By zhaopeihua
variant allele fraction

hi:
What are "variant allele fraction" when talking about somatic mutations?
Forum: Bioinformatics 09-11-2013, 12:26 AM
Replies: 0
Views: 1,204
Posted By zhaopeihua
detecting mutation from RNA seq data

Hi:

I am new to the RNA-seq,I want to find out somatic mutations from RNA-seq data, Can anyone show me how to do it ?
Thanks!
Forum: Metagenomics 08-30-2013, 11:14 PM
Replies: 1
Views: 2,623
Posted By zhaopeihua
how to make a matrix of OTU abundance in each sample

hi all,
I'm doing some analysis in 454 data. I have picked Operational Taxonomic Units (OTUs) based on sequence similarity within the reads, and picked a representative sequence from each...
Forum: Metagenomics 08-28-2013, 08:22 PM
Replies: 0
Views: 2,250
Posted By zhaopeihua
mothur extract the .flow data from sff file

Hi all,

I'm totally new in this area,i hava got some 454 16s data run through mothur. follow by the standard operating procedure (SOP) that the Schloss lab uses to process their 16S rRNA...
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