SEQanswers

Go Back   SEQanswers > Applications Forums > Epigenetics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Can Cuffdiff treat paired-end and single-end reads at the same time? zun RNA Sequencing 3 06-12-2012 05:37 PM
Can paired-end mapping produce more reads than single-end ? warrenemmett Bioinformatics 13 03-20-2012 11:10 PM
Paired-end Bam from single-end aligned sam ramouz87 Bioinformatics 4 08-17-2011 12:55 PM
RNA-seq: Replicates, single-end, paired-end story pasta Bioinformatics 2 07-04-2011 11:51 PM
Does Cufflinks support single-end and paired end data together ? ersenkavak Bioinformatics 1 10-22-2010 07:26 AM

Reply
 
Thread Tools
Old 01-31-2011, 12:07 PM   #1
analyst
Member
 
Location: US

Join Date: Jan 2011
Posts: 18
Default which is better, paired or single end

Can anyone please answer these

For chip-seq and RNA-seq, which is better PE or SE

In one lane in illumina, one gets ~15 GB sequence which is 5X for human. Is this enough for chip-seq and RNA seq, or should one run multiple lanes.

Is it good idea to multiplex in the above experiment if budget is constraint.

Thanks in advance for you valuable time. It will be a big help really.
analyst is offline   Reply With Quote
Old 02-08-2011, 03:17 PM   #2
edawad
Member
 
Location: bay area

Join Date: Mar 2010
Posts: 10
Default

PE is almost always better for RNA-seq--you gain more information about splice junctions etc. It doesn't hurt for ChIP-Seq and may help you better identify enriched binding sites in repetitive regions (although some mappers may not be able to handle PE tags).

For most ChIP-Seq applications 10-15 million reads is enough (unless it's a histone or highly ubiquitous TF). You can computationally determine your ChIP-Seq coverage/saturation using a program like MACS --diag option. I can't say much for RNA-Seq but somewhere out there I've seen a table with suggested sequence coverage. RNA-Seq probably requires more reads than ChIP-Seq, moreso if you plan on getting quantitative information out of it.
edawad is offline   Reply With Quote
Old 02-10-2011, 02:56 PM   #3
SeqAA
Guest
 

Posts: n/a
Default

PE for RNA Seq
SE for ChIP Seq. There really isn't the need for Paired reads.

the throughput really varies on the experiment. Histone modifications or TF analysis?
  Reply With Quote
Old 08-29-2011, 11:24 PM   #4
sciencewu
Member
 
Location: china

Join Date: Dec 2010
Posts: 12
Default

SE is better for you .
sciencewu is offline   Reply With Quote
Old 08-30-2011, 11:00 AM   #5
bioinfosm
Senior Member
 
Location: USA

Join Date: Jan 2008
Posts: 482
Default

SE is faster and cheaper... PE on the other hand is more data, and theoretically more efficient, provided you use the appropriate methods to make use of paired information
__________________
--
bioinfosm
bioinfosm is offline   Reply With Quote
Old 10-05-2011, 11:28 AM   #6
yxibcm
Junior Member
 
Location: houston

Join Date: Jun 2010
Posts: 6
Default

Actually, I would suggest using PE for ChIP-seq too. For SE reads, existing ChIP-seq software, such as MACS, shift and extend the reads to build the whole genome profile. The shift and extend distance was a fixed value estimated from the double peak pattern or provided by command line parameters. This might be inaccurate if the wrong shift/extend distance were used, and might cause the peak appear as doublets. So the peak heights are sensitive to the shift/extend values. PE sequencing provides fragment size information, therefore build whole genome profile is straightforward, no shift or extend involved. PE is also not that expensive compared with SE.

Quote:
Originally Posted by SeqAA View Post
PE for RNA Seq
SE for ChIP Seq. There really isn't the need for Paired reads.

the throughput really varies on the experiment. Histone modifications or TF analysis?

Last edited by yxibcm; 10-05-2011 at 11:34 AM.
yxibcm is offline   Reply With Quote
Old 10-05-2011, 11:34 AM   #7
ETHANol
Senior Member
 
Location: Western Australia

Join Date: Feb 2010
Posts: 310
Default

Are there peak callers that accept paired-end data?
__________________
--------------
Ethan
ETHANol is offline   Reply With Quote
Old 10-05-2011, 11:45 AM   #8
ETHANol
Senior Member
 
Location: Western Australia

Join Date: Feb 2010
Posts: 310
Default

A little searching answers that question:

http://www.biomedcentral.com/1471-2105/11/81
http://www.ebi.ac.uk/~swilder/SWEMBL/
http://liulab.dfci.harvard.edu/MACS/README.html

And maybe some others.
__________________
--------------
Ethan
ETHANol is offline   Reply With Quote
Old 10-05-2011, 10:32 PM   #9
mudshark
Senior Member
 
Location: Munich

Join Date: Jan 2009
Posts: 138
Default

second that. at least it would be helpful to have one corresponding PE run to see how uneven fragment size distribution along the genome is. in addition the fragment size knowledge might provide important information on local chromatin structure. have a look at: www.ncbi.nlm.nih.gov/pubmed?term=21131275

Quote:
Originally Posted by yxibcm View Post
Actually, I would suggest using PE for ChIP-seq too. For SE reads, existing ChIP-seq software, such as MACS, shift and extend the reads to build the whole genome profile. The shift and extend distance was a fixed value estimated from the double peak pattern or provided by command line parameters. This might be inaccurate if the wrong shift/extend distance were used, and might cause the peak appear as doublets. So the peak heights are sensitive to the shift/extend values. PE sequencing provides fragment size information, therefore build whole genome profile is straightforward, no shift or extend involved. PE is also not that expensive compared with SE.
mudshark is offline   Reply With Quote
Reply

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 01:30 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO