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Search: Posts Made By: yueli
Forum: Bioinformatics 08-28-2019, 05:13 AM
Replies: 4
Views: 830
Posted By yueli
Hello, SapirP, Thank you so much for your...

Hello, SapirP,

Thank you so much for your answer.

Thank you for the clue you give to me.

Thank you again!

With Best,
Forum: Bioinformatics 08-04-2019, 11:36 AM
Replies: 4
Views: 830
Posted By yueli
Hello, SNPsaurus, Thank you so much for your...

Hello, SNPsaurus,

Thank you so much for your replying.

I want to know the DNA sequencing which can binding to the protein.

Thank you in advance for your great help!

Best,
Forum: Bioinformatics 08-04-2019, 10:40 AM
Replies: 4
Views: 830
Posted By yueli
protein dna binding sites

Hello,

I have around 200 protein's fasta file. How can I find these proteins binding site with DNA?

For example:It comes from Wikipedia.

The AP-1 binding site, also known as the AP-1...
Forum: Bioinformatics 07-31-2019, 11:43 AM
Replies: 2
Views: 670
Posted By yueli
Hello, Meyana, Thank you for your response! ...

Hello, Meyana,

Thank you for your response!

Thank you!

Best,

Yue
Forum: Bioinformatics 07-28-2019, 09:55 AM
Replies: 2
Views: 670
Posted By yueli
software can draw this picture

Hello,

Anyone who know which software can draw this picture?

Is that possible I can draw this picture by Infopath which is a package in Microsoft office?

Thanks in advance?

Yue
Forum: Bioinformatics 07-01-2019, 05:00 PM
Replies: 0
Views: 366
Posted By yueli
chip-seq visualize tool IGV

Hello,

I tried to use IGV to visualize my chip-seq peak file.

Why it is so strange? The peak is not smooth?

Thanks in advance for any help!

Best,
Forum: Bioinformatics 07-01-2019, 04:48 PM
Replies: 2
Views: 359
Posted By yueli
Hello, Colindaven, Thank you so much for...

Hello, Colindaven,

Thank you so much for your great help!

Best,

Yue
Forum: Bioinformatics 06-30-2019, 03:35 PM
Replies: 2
Views: 359
Posted By yueli
makeBigWig.pl

Hello, I

I tried to use makeBigWig.pl

Acutally, bedGraphToBigWig has installed.

Thanks for any help!

Yue
Forum: Illumina/Solexa 06-22-2019, 09:31 AM
Replies: 2
Views: 1,372
Posted By yueli
Hello, @KB Flollwing is my command, qvalue...

Hello, @KB

Flollwing is my command, qvalue cutoff = 5.00e-02. I got peaks around 400.




If using paired end reads use “--format BAMPE” to let MACS2 pileup the whole
fragments in general....
Forum: Bioinformatics 06-04-2019, 12:01 PM
Replies: 0
Views: 358
Posted By yueli
annotation the gene is a promoter

Hello,

I have many human genes. How can I annotation these genes are promoters or not?

Which database or software I can use?

Thanks in advance for any help!

Best regards!
Forum: Illumina/Solexa 04-27-2019, 08:42 AM
Replies: 1
Views: 567
Posted By yueli
summits.bed

summits.bed
Forum: Illumina/Solexa 04-25-2019, 01:27 PM
Replies: 1
Views: 567
Posted By yueli
which file I can use for finding motifs

Hello,

I want to find the motifs of chip-seq data. Which files I can use?

1. the file of *.narrowPeak after peak calling?

2. the *.fa of the genes after annotation of the peaks?

Thanks...
Forum: Illumina/Solexa 04-06-2019, 01:23 PM
Replies: 0
Views: 360
Posted By yueli
motif comparation

Hello,

I predict some motifs by findmotifsgenome.pl (homer), meme-chip and RSAT website, and want to finding the overlapping.

Is there any tools or software can compare the motifs?

Thanks...
Forum: Illumina/Solexa 04-01-2019, 03:17 PM
Replies: 1
Views: 604
Posted By yueli
every time open the terminal nano...

every time open the terminal

nano ~/.bash_profile

PATH=$PATH:/home/administrator/homer/bin

ctrlX

Y
Forum: Illumina/Solexa 04-01-2019, 12:53 PM
Replies: 1
Views: 604
Posted By yueli
running findMotifsGenome.pl error

Hello,

I am running findMotifGenome.pl in homer package.

Any help is appreciated!

With Best!

Yue Li
Forum: Illumina/Solexa 03-31-2019, 10:22 AM
Replies: 2
Views: 500
Posted By yueli
atpoint, Thank you so much for your great...

atpoint,

Thank you so much for your great help!
Forum: Illumina/Solexa 03-29-2019, 07:20 AM
Replies: 2
Views: 500
Posted By yueli
which one is best for motif discobery in human paired-ends chip-seq?

Hello,

I am working on human paired-ends chip-seq data analysis.

Which software or web tools is the best for motif discovery?

Thanks in advance!

With Best!
Forum: Illumina/Solexa 03-20-2019, 02:28 PM
Replies: 2
Views: 1,372
Posted By yueli
which one is better for paired-ends peak calling? MACS2 OR MACS14?

Hello,

I'am working on paired-ends chip-seq analysis.

Which one is better for peak calling? macs2 OR macs14?

I ran both of them, macs2 has less peaks than macs14.

Thanks in advance for...
Forum: Bioinformatics 05-11-2018, 08:54 AM
Replies: 0
Views: 531
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: 1,160
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: 1,342
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: 749
Posted By yueli
./STAR works

./STAR works
Forum: Illumina/Solexa 04-25-2018, 08:45 AM
Replies: 1
Views: 749
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: 6,435
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: 647
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
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