IP library vs Input library reads number

badribio · 12-01-2014, 01:27 PM

Hi,
I am newbies in this forum and this is my first post. I have recently performed H3K4me3 ChIP librairies preparation with using NEXTflex ChIP-Seq kit to sequencing 18 Immunoprecipitation products (IPs)and 6 inputs as negatives controls.
This sequencing is achieved on 3 Illumina Rapid flow cells with PE 2X50 pb reads. 3 IPs and 1 input have been sequenced in the same lane onto HiSeq 2500 with the new version of HCS 2.2.38 software. After Casava demultiplexing, I have getting 80 to 100 million reads with IP librairies and 30-36 million reads for input librairies. I have used 5% PhiX as a balanced genome for this experience because I have get a good results last time when we used 1% PhiX with the old HCS version.
Can you help me please to understand this result.

Thanks a lot.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
fewer reads after Input library sequencing	badribio	Epigenetics	0	12-01-2014 01:24 PM
Did low input library and traditional library generated RNAseq data can be compared?	bioinforD	Bioinformatics	6	11-25-2013 07:57 AM
PacBio RS II Library Prep Input	JoeChris38	Pacific Biosciences	1	10-15-2013 03:32 PM
Library Prep with Low Input	Joltex	Ion Torrent	6	12-11-2012 01:13 PM
Number of Reads in 454 Library	foolishbrat	454 Pyrosequencing	5	09-09-2009 03:12 AM

12-01-2014, 01:27 PM	#1
badribio Junior Member Location: France Join Date: Mar 2011 Posts: 2	IP library vs Input library reads number Hi, I am newbies in this forum and this is my first post. I have recently performed H3K4me3 ChIP librairies preparation with using NEXTflex ChIP-Seq kit to sequencing 18 Immunoprecipitation products (IPs)and 6 inputs as negatives controls. This sequencing is achieved on 3 Illumina Rapid flow cells with PE 2X50 pb reads. 3 IPs and 1 input have been sequenced in the same lane onto HiSeq 2500 with the new version of HCS 2.2.38 software. After Casava demultiplexing, I have getting 80 to 100 million reads with IP librairies and 30-36 million reads for input librairies. I have used 5% PhiX as a balanced genome for this experience because I have get a good results last time when we used 1% PhiX with the old HCS version. Can you help me please to understand this result. Thanks a lot.