SEQanswers

Go Back   SEQanswers > Search Forums


Showing results 1 to 9 of 9
Search took 0.00 seconds.
Search: Posts Made By: Huijuan
Forum: Bioinformatics 02-27-2012, 05:11 PM
Replies: 0
Views: 840
Posted By Huijuan
About RNA-Seq data

Hi all
Now I want to collect some RNA-Seq data to do some analysis about cancer before experiments.And I am a totally green hand of this area. So besides SRA,Is there any other ways to get...
Forum: Bioinformatics 04-30-2011, 10:14 PM
Replies: 1
Views: 4,437
Posted By Huijuan
my understanding for cuffdiff output

Hi. I am a newbie in RNA-Seq analysis and now I am doing the pipeline with several software. I want to use cufflinks ,cuffcompare and cuffdiff to get DE genes,alternative splicing and novel...
Forum: RNA Sequencing 04-28-2011, 10:31 PM
Replies: 12
Views: 5,330
Posted By Huijuan
there‘s a method saying that you can keep the tmp...

there‘s a method saying that you can keep the tmp files when you run Tophat by the parameter --keep-tmp then you will get both sam and bam files
Forum: Bioinformatics 04-26-2011, 06:29 PM
Replies: 1
Views: 2,461
Posted By Huijuan
How to evaluate the RNA-Seq analysis software I choose?

Hi,I am a newbie here, I want to get familiar with the RNA-Seq pipeline and so I choose several softwares in each step like Bowtie,BWA,TopHat with mapping and DEGseq,Cufflinks with DE analysis.But...
Forum: RNA Sequencing 04-26-2011, 04:57 PM
Replies: 12
Views: 5,330
Posted By Huijuan
This time I didn't use viewSam.jar and just used...

This time I didn't use viewSam.jar and just used awk and grep to get them apart and then did counting
Forum: RNA Sequencing 04-26-2011, 04:41 PM
Replies: 12
Views: 5,330
Posted By Huijuan
Ive figured out the reason.Thanks so much for...

Ive figured out the reason.Thanks so much for helping.
Forum: RNA Sequencing 04-19-2011, 07:47 PM
Replies: 12
Views: 5,330
Posted By Huijuan
Here's the problem I use the way you told me...

Here's the problem
I use the way you told me with the mapping results with BWA. And the total number of unaligned reads, uniquely mapped reads and multireads is not equal to the total number of...
Forum: RNA Sequencing 04-16-2011, 05:11 PM
Replies: 12
Views: 5,330
Posted By Huijuan
Many thanks for helping.I did as what you said...

Many thanks for helping.I did as what you said and got what I want.Thank you again
Huijuan
Forum: RNA Sequencing 04-16-2011, 05:19 AM
Replies: 12
Views: 5,330
Posted By Huijuan
Question analysis after mapping

Hi,I'm a beginner in RNA-Seq analysis,now I've mapped the short reads with Bowtie,TopHat and other softwares,I'm trying to analyze the mapping efficiency by counting the uniquely mapped...
Showing results 1 to 9 of 9

 


All times are GMT -8. The time now is 10:14 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO