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Search: Posts Made By: HSV-1
Forum: Bioinformatics 01-19-2016, 06:52 PM
Replies: 0
Views: 835
Posted By HSV-1
Red face How to Scan Degenerate DNA motifs (TF binding sites)

Hi all,
I am interested in the genome-wide DNA motifs for transcription factors.
I am wondering if there are softwares I can use to scan degenerate DNA motifs.
For example I want to search ...
Forum: Bioinformatics 09-27-2014, 09:25 PM
Replies: 11
Views: 36,525
Posted By HSV-1
You guys save my ass, thanks!

You guys save my ass, thanks!
Forum: Sample Prep / Library Generation 07-10-2014, 07:03 PM
Replies: 3
Views: 1,704
Posted By HSV-1
Smile yes, treat as the reverse crosslinked chromatin...

yes, treat as the reverse crosslinked chromatin as PCR.
good good luck
Forum: Sample Prep / Library Generation 07-09-2014, 05:58 PM
Replies: 3
Views: 1,704
Posted By HSV-1
Hi, I had the same trouble for long but now I...

Hi,
I had the same trouble for long but now I solved the problem.
In short the whole cell lysate is no problem.
You thought your samples were not sonicated well according to your Agarose...
Forum: Illumina/Solexa 07-04-2014, 11:15 PM
Replies: 3
Views: 3,494
Posted By HSV-1
Thumbs up Thanks ! I will be careful with the coming...

Thanks ! I will be careful with the coming experiments.

More questions:
Once ChIP DNA is purified how long it could be stored at -80 (a few weeks) or Liquid nitrogen(forever)?

How...
Forum: Illumina/Solexa 07-03-2014, 01:14 AM
Replies: 3
Views: 3,494
Posted By HSV-1
Angry ChIP qPCR vs ChIP-seq

Hi ,

We have performed Chromatin immunoprecipitation experiments.
Our goal is to find out the genome-wide bindings of a transcription factor so we sent our ChIP-qPCR validated sample to do the...
Forum: RNA Sequencing 10-31-2013, 06:43 PM
Replies: 2
Views: 1,437
Posted By HSV-1
I have done some analyses. Eventually we didn't...

I have done some analyses.
Eventually we didn't go further. There are many rare bases (many are modified ) on tRNA.
These definitely are problems for reverse transcription and therefore for ...
Forum: Bioinformatics 09-25-2013, 06:19 AM
Replies: 0
Views: 866
Posted By HSV-1
Unhappy pick out conserved introns between drosophila and Human

Hi, folks

I am interested in intron evolution. I have collected drosophila introns,... human introns, mouse introns....

I want to extract the conserved introns between drosophila and human. ...
Forum: RNA Sequencing 09-15-2013, 08:00 PM
Replies: 3
Views: 2,844
Posted By HSV-1
Thanks, Dario. How can I output a fastq file...

Thanks, Dario.
How can I output a fastq file at this point ?
Forum: RNA Sequencing 09-14-2013, 08:58 PM
Replies: 3
Views: 2,844
Posted By HSV-1
Cool How to Pick out reads from certain locus

Hi, all
I want to see all the reads derived from TP53 in a RNA-seq dataset.
How to do this?

I have searched the forum I didn't find the similar post.


Thanks!
Forum: Illumina/Solexa 09-11-2013, 03:39 AM
Replies: 9
Views: 3,429
Posted By HSV-1
Thumbs up Thanks. thank you very much.

Thanks. thank you very much.
Forum: Illumina/Solexa 09-11-2013, 03:31 AM
Replies: 9
Views: 3,429
Posted By HSV-1
Thanks for your reply. I have the original...

Thanks for your reply. I have the original rna-seq data in *.fastq format.
is grep the linux function? what are -B and -A 2 for?

Thank you guys!
Forum: Illumina/Solexa 09-11-2013, 03:01 AM
Replies: 9
Views: 3,429
Posted By HSV-1
Smile How to Pick certain reads out of RNA-seq data to a fasta file?

Hello, every one.
I tried searching the solution to my question. But I couldn't . So put a new thread here. What I want to do is to pick out all the reads by Illumina Hiseq that contain the...
Forum: Bioinformatics 02-05-2013, 06:15 AM
Replies: 3
Views: 991
Posted By HSV-1
How to count the repeating times of a certain 11bp long sequence

Hi, all
I want to count the repeating times of an 11bp long sequence(for example: tcgtgacggta ) in human and mouse genome. Further I need know the positions of this sequence located in. This 11bp...
Forum: RNA Sequencing 12-05-2012, 11:32 PM
Replies: 6
Views: 2,262
Posted By HSV-1
If so what I don't understand is what is the...

If so what I don't understand is what is the advantage of pair-end reads over single end reads? It seems to me that there is no much and significant difference between them considering each pair...
Forum: RNA Sequencing 12-05-2012, 10:41 PM
Replies: 6
Views: 2,262
Posted By HSV-1
Thans for response. Good point. Is left reads...

Thans for response. Good point.
Is left reads file normally suffixed with _1 and right ones with _2?
Forum: RNA Sequencing 12-05-2012, 07:48 PM
Replies: 6
Views: 2,262
Posted By HSV-1
Can I treat pair-end reads as single end reads replicates?

I think mapping is no problem. Most of my pair-end reads were not mappable by Tophat. Only 15% of reads are mappble. By treating them as single end I could map more than 15%.
What is the potential...
Forum: Bioinformatics 11-16-2012, 04:48 PM
Replies: 10
Views: 2,670
Posted By HSV-1
I didn't know your reads are from roche 454. ...

I didn't know your reads are from roche 454.
There is special protocol for long reads.
Forum: RNA Sequencing 11-10-2012, 06:28 PM
Replies: 0
Views: 1,149
Posted By HSV-1
RNA-seq in shRNA treated cells

Hi all,
I am doing RNA-seq in shRNA treated cells.
Can I expect in RNA-seq data there is less shRNA target gene RNA abundance than the shRNA control?

However I read a few articles saying that...
Forum: Bioinformatics 10-24-2012, 02:01 AM
Replies: 10
Views: 2,670
Posted By HSV-1
sort of normal. be sure your que is tolerant...

sort of normal.
be sure your que is tolerant for this comsumed time or it will be killed w/o accomplishment.
Forum: Bioinformatics 10-22-2012, 05:33 PM
Replies: 10
Views: 2,670
Posted By HSV-1
at which step? when tophat is writing segment,...

at which step?
when tophat is writing segment, junction files, it will take a few days or even a week.
Forum: General 10-19-2012, 05:48 PM
Replies: 5
Views: 3,864
Posted By HSV-1
This is probably the reason. How to fix? ...

This is probably the reason.
How to fix?
From the same sequence data with ensemble gft I should get more accepted hits by tophat .
Forum: General 10-18-2012, 06:39 AM
Replies: 5
Views: 3,864
Posted By HSV-1
the same is much bigger than the one from ucsc,...

the same is much bigger than the one from ucsc, why?
Forum: Bioinformatics 10-18-2012, 06:34 AM
Replies: 10
Views: 2,670
Posted By HSV-1
did you put "--no-coverage-search"? if not it...

did you put "--no-coverage-search"? if not it will take very long time.
Forum: RNA Sequencing 10-16-2012, 09:06 PM
Replies: 2
Views: 2,781
Posted By HSV-1
This has been worrying me for long. Any...

This has been worrying me for long. Any experience will help.
Thanks .
Showing results 1 to 25 of 38

 


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