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Search: Posts Made By: qqtwee
Forum: Bioinformatics 08-16-2012, 02:28 AM
Replies: 15
Views: 16,276
Posted By qqtwee
how does cufflinks to estimate the distribution of fragment lengths?

Hello, Do you know how can I know the insert size? I see you say can use cufflinks, could you tell that how does cufflinks to estimate the distribution of fragment lengths in detail? Thank you very...
Forum: General 07-31-2012, 12:43 AM
Replies: 6
Views: 3,809
Posted By qqtwee
Hi, are there any good places to find freely...

Hi, are there any good places to find freely RNA-seq data of all or many different human cell lines ,and RNA-seq data of all or many different human tissue? If NCBI database can find this, how can I...
Forum: Bioinformatics 07-26-2012, 08:13 PM
Replies: 3
Views: 2,698
Posted By qqtwee
differential gene expression analysis between Different strains by RNA-seq

Hello,
I work with solexa paired-end RNA-seq data of bacteria. I analyze differential gene expression by FPKM from cufflinks,and analyze FPKM using DEGseq to get differential expression genes. I...
Forum: Bioinformatics 07-26-2012, 07:53 PM
Replies: 0
Views: 878
Posted By qqtwee
question with cufflinks applying in bacteria

Hello, I am dealing with solexa pared-end RNA-seq data of bacteria. Now I use cufflinks tools to caculate FPKM, then I can analyze differential expression genes, but when I compare FPKM value and...
Forum: Bioinformatics 07-26-2012, 07:32 PM
Replies: 10
Views: 5,616
Posted By qqtwee
I download the data with the selection of fltered...

I download the data with the selection of fltered download,and then select FASTQ format. BTW, there are two ways that we can get FASTQ format,the one is directly download FASTQ format like that from...
Forum: Bioinformatics 07-25-2012, 07:59 PM
Replies: 10
Views: 5,616
Posted By qqtwee
SRA database fastq format

Hello, I want to ask a quenstion:when I directly download FASTQ format from SRA database, it looks like this, as follows, I want to know how can I convert it to an available data to analyse it...
Forum: Bioinformatics 05-09-2012, 08:30 PM
Replies: 4
Views: 2,164
Posted By qqtwee
Hello, I am analying bacterial transcriptome...

Hello, I am analying bacterial transcriptome using solexa paired-end strand specific (SOLiD adapter library) sequencing data, I have no idea how to deal with it. Could you give me some advice on...
Forum: Introductions 05-09-2012, 08:19 PM
Replies: 2
Views: 2,672
Posted By qqtwee
Hello, do you know how deal with the...

Hello, do you know how deal with the strand-specific RNA-seq data? which tools has the option for strand-specific information? Looking forward to your reply! Thank you! Best wishes!
Forum: RNA Sequencing 05-09-2012, 07:08 PM
Replies: 7
Views: 5,747
Posted By qqtwee
Thank you for your reply! Do you know BWA has...

Thank you for your reply! Do you know BWA has option that can treat reads in a strand specific ?
Forum: Bioinformatics 05-09-2012, 06:36 AM
Replies: 11
Views: 9,326
Posted By qqtwee
how can I take the strand info into account

Hello, now my data is strand specific paired end RNA-seq,could you tell me how can I take the strand info into account when I do mapping with BWA? Is there some parameter in BWA that deal with the...
Forum: RNA Sequencing 05-09-2012, 05:54 AM
Replies: 1
Views: 4,726
Posted By qqtwee
strand specific RNA-seq mapping

Does anyone know how do mapping for strand specific RNA-seq data? which tools can work well? what the parameter of tools for strand specific infomation of RNA-seq data?
Looking forward to your...
Forum: RNA Sequencing 05-09-2012, 05:53 AM
Replies: 7
Views: 5,747
Posted By qqtwee
strand specific RNA-seq mapping

Does anyone know how do mapping for strand specific RNA-seq data? which tools can work well? what the parameter of tools for strand specific infomation of RNA-seq data?
Looking forward to your...
Forum: Bioinformatics 03-23-2012, 02:18 AM
Replies: 7
Views: 4,638
Posted By qqtwee
would you like to tell me how do you done it...

would you like to tell me how do you done it successfully? I have the same error!
Thanks!
Best wishes!
Forum: Bioinformatics 11-24-2011, 11:04 PM
Replies: 53
Views: 68,007
Posted By qqtwee
cufflinks Error

Hello,all
when I use cufflinks without a gtf file for bacterial RNA-seq, I get the follow result:...
Forum: Bioinformatics 11-11-2011, 08:03 PM
Replies: 0
Views: 1,651
Posted By qqtwee
help about cufflinks for bacterial rna-seq data

Hi,recently I am analysing bacterial rna-seq data from illumina GAII.Iwant to use cufflinks to caculate RPKM, I select the default options and get the result file as follow:...
Forum: Bioinformatics 10-24-2011, 01:01 AM
Replies: 12
Views: 6,660
Posted By qqtwee
the same error,need help! thanks!

the same error,need help! thanks!
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