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Search: Posts Made By: yueli
Forum: Illumina/Solexa 06-22-2019, 09:31 AM
Replies: 2
Views: 594
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: 199
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: 386
Posted By yueli
summits.bed

summits.bed
Forum: Illumina/Solexa 04-25-2019, 01:27 PM
Replies: 1
Views: 386
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: 254
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: 333
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: 333
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: 378
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: 378
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: 594
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: 468
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: 1,090
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: 1,151
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: 654
Posted By yueli
./STAR works

./STAR works
Forum: Illumina/Solexa 04-25-2018, 08:45 AM
Replies: 1
Views: 654
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: 4,707
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: 574
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: 4,707
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: 4,707
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: 667
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: 890
Posted By yueli
Thanks for GenoMax!

Thanks for GenoMax!
Forum: Illumina/Solexa 04-20-2018, 06:10 AM
Replies: 5
Views: 890
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: 890
Posted By yueli
Thanks for GenoMax!

Thanks for GenoMax!
Forum: Illumina/Solexa 04-19-2018, 01:52 PM
Replies: 5
Views: 890
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: 1,162
Posted By yueli
Thanks for GenoMax response!

Thanks for GenoMax response!
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