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Search: Posts Made By: yueli
Forum: Bioinformatics 05-11-2018, 08:54 AM
Replies: 0
Views: 264
Posted By yueli
edgeR DESeq2

Hello,

I used the edgeR and DESeq2 to calculate the differentially expressed genes.

Of course, the results are not identical. I read many papers, and both of the packages are evaluated quite...
Forum: RNA Sequencing 04-29-2018, 08:28 AM
Replies: 1
Views: 835
Posted By yueli
sequence dupliaction in FastQc report

Hello,

I found my sequence duplication level is high in my FastQc report.

Do I have to use MarkDuplicates?

Thanks in advance!
Forum: RNA Sequencing 04-25-2018, 02:33 PM
Replies: 1
Views: 741
Posted By yueli
error in STAR

Hello,

When I ran STAR, it happens like this:

Anyone has suggestion?

Thanks in advance for great help!


yue
Forum: Illumina/Solexa 04-25-2018, 09:20 AM
Replies: 1
Views: 450
Posted By yueli
./STAR works

./STAR works
Forum: Illumina/Solexa 04-25-2018, 08:45 AM
Replies: 1
Views: 450
Posted By yueli
install of STAR

Hello,

I downloaded the STAR-2.6.0a from https://github.com/alexdobin/STAR/releases, following the file README.md. It looks has compiled.

cd STAR/source

make STAR

When I ran this program,...
Forum: Illumina/Solexa 04-25-2018, 06:25 AM
Replies: 4
Views: 1,280
Posted By yueli
r.rosati, Thanks for helping!

r.rosati,

Thanks for helping!
Forum: Illumina/Solexa 04-24-2018, 04:33 AM
Replies: 0
Views: 387
Posted By yueli
remove rRNA

Hello,

Human RNA-seq data, after remove adaptor and primer, do I need to remove rRNA?

Thanks in advance for great help!

Yue Li
Forum: Illumina/Solexa 04-24-2018, 04:27 AM
Replies: 4
Views: 1,280
Posted By yueli
Thank you so much GenoMax!

Thank you so much GenoMax!
Forum: Illumina/Solexa 04-21-2018, 09:45 AM
Replies: 4
Views: 1,280
Posted By yueli
phred 33 or 64

Hello,

I am trying to use Trimmomatic to trim adaptor, and really confusing about my file is phred +33 or phred +64?


@J00160:122:HT2VJBBXX:8:1101:23348:1261 1:N:0:ATTACTCG+AGGCNATA...
Forum: Illumina/Solexa 04-20-2018, 01:22 PM
Replies: 0
Views: 540
Posted By yueli
adaptor and primer from fastqc

Hello,

My file is Clean fastq file from Illumina HiSeq 3000 with 2X100 cycles run.

When ran fastqc, they have over-represented sequence of adaptor and primer.

What can I do?

Thanks in...
Forum: Illumina/Solexa 04-20-2018, 12:17 PM
Replies: 5
Views: 685
Posted By yueli
Thanks for GenoMax!

Thanks for GenoMax!
Forum: Illumina/Solexa 04-20-2018, 06:10 AM
Replies: 5
Views: 685
Posted By yueli
Thanks for GenoMax's response! Actually I...

Thanks for GenoMax's response!

Actually I really do not know the adaptor of my file. My fastq file is human RNA-seq dataset generated from Illumina HiSeq 3000 with 2X100 cycles run.

What can I...
Forum: Illumina/Solexa 04-20-2018, 04:27 AM
Replies: 5
Views: 685
Posted By yueli
Thanks for GenoMax!

Thanks for GenoMax!
Forum: Illumina/Solexa 04-19-2018, 01:52 PM
Replies: 5
Views: 685
Posted By yueli
trim adaptor Illumina

Hello,

Human RNA-seq dataset was generated from Illumina HiSeq 3000 with 2X100 cycles run.

Do I have to trim the adaptor?

Thanks in advance for great help!

Sincerely,
Forum: Illumina/Solexa 04-19-2018, 07:16 AM
Replies: 2
Views: 554
Posted By yueli
Thanks for GenoMax response!

Thanks for GenoMax response!
Forum: Bioinformatics 04-19-2018, 06:42 AM
Replies: 1
Views: 615
Posted By yueli
suitable aligner for human RNA-seq

Hello,

Human RNA-seq dataset was generated from Illumina HiSeq 3000 with 2X100 cycles run.

The first step is making alignment of the reads to the human genome. These are many aligner, such as:...
Forum: Illumina/Solexa 04-19-2018, 06:37 AM
Replies: 2
Views: 554
Posted By yueli
best suitable aligner for RNA-seq mapping

Hello,

Human RNA-seq dataset was generated from Illumina HiSeq 3000 with 2X100 cycles run.

The first step is making alignment of the reads to the human genome. These are many aligner, such as:...
Forum: Bioinformatics 10-17-2015, 06:10 AM
Replies: 2
Views: 676
Posted By yueli
Hi, Thanks! GenoMax. Thank you so much! ...

Hi,

Thanks! GenoMax. Thank you so much!

It works when open:

http://www.ncbi.nlm.nih.gov/public/?/ftp/sra/sra-instant/reads/ByRun/sra/SRR/SRR955/SRR955511

I appreciated!
Forum: Bioinformatics 10-17-2015, 04:17 AM
Replies: 2
Views: 676
Posted By yueli
use aspera download sra data

Hi,

I have already installed aspera. How can I use it to down data from sra datasets?

Please see attachment. I clicked download, no response.

Thanks in advance for great help!

yue
Forum: Bioinformatics 07-16-2015, 07:47 PM
Replies: 0
Views: 512
Posted By yueli
DESeq pvalue>0.05 qvalue=1

Hi,

I try to DESeq find the differentially expressed genes in two samples.

The result is all the pvalue>0.05, and qvalue=1.

Any suggestion or advice?

Thanks for great help!
Forum: Bioinformatics 07-15-2015, 11:49 PM
Replies: 0
Views: 470
Posted By yueli
fisher test differentially gene

Hi,

I want to find the differentially expressed genes. The fiel has attached.

Anyone has ideas to use fisher test to find out the differentially expressed genes? Any software or tools?
...
Forum: Bioinformatics 07-15-2015, 08:18 PM
Replies: 0
Views: 456
Posted By yueli
differentially expressed mRNA pvalue FDR value

Hi,

I have two transcriptomes mRNA samples which already have their FPKM value. Want to find theri differentially expressed mRNA.

How can I calculate their p value and FDR value?



Any...
Forum: Bioinformatics 07-15-2015, 05:35 PM
Replies: 2
Views: 564
Posted By yueli
Thanks, blancha! Your answer really help me....

Thanks, blancha!

Your answer really help me. I appreciate!

Yue
Forum: Bioinformatics 07-14-2015, 11:56 PM
Replies: 3
Views: 661
Posted By yueli
Thanks, mastal, GenoMax. You are right!

Thanks, mastal, GenoMax.

You are right!
Forum: Bioinformatics 07-14-2015, 11:50 PM
Replies: 2
Views: 564
Posted By yueli
the usage of qvalue

hi,

I just want to import my data in the package qvalue under R environment.

The file name is test_soma.txt.

The data format is just as follow:


0.0642720365
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