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Forum: Illumina/Solexa 06-21-2019, 07:48 AM
Replies: 2
Views: 1,342
Posted By KB*
Hi, @Yue Li Did you find an answer for your...

Hi, @Yue Li

Did you find an answer for your question?

I am analysing ChIP-Seq data and I used MACS2. How may peaks did you get? I had to use q=0.005 (minimum FDR (q-value) cutoff for peak...
Forum: Bioinformatics 06-10-2019, 05:59 AM
Replies: 2
Views: 812
Posted By KB*
@frascom Than you! I figured that up. I used...

@frascom

Than you! I figured that up. I used institutional internet with wired access to the internet. And it was fast :)) wifi is much slower. In particular from a private (home) network.

I am...
Forum: Sample Prep / Library Generation 06-10-2019, 03:03 AM
Replies: 3
Views: 947
Posted By KB*
Hi, Dina, yes, I used 98 uL (0.8X), just as...

Hi, Dina,

yes, I used 98 uL (0.8X), just as it is described in the kit manual.

I am a bit concerned about your fragments length. Are not they a bit longer than it is needed? E.g. 600bp. When I...
Forum: Sample Prep / Library Generation 06-08-2019, 04:27 AM
Replies: 3
Views: 947
Posted By KB*
Hi, Sorry, it is a bit late reply. I hope...

Hi,

Sorry, it is a bit late reply. I hope you solved your problem.

I used NEBNext Ultra DNA lib prep kit and it worked OK for me. I guess you might not have enough DNA to start with. Did you...
Forum: Bioinformatics 06-08-2019, 04:10 AM
Replies: 2
Views: 812
Posted By KB*
My NGS data. What to use: galaxy, R or ?

Hi all,

Really hope for your help, guys.

I finally got my ChIP-Seq data back. Hoping it is not too bad. You can check for the history of my libraries prep here:
...
Forum: Illumina/Solexa 05-06-2019, 05:35 PM
Replies: 0
Views: 695
Posted By KB*
Pooling libs. for Novaseq. How many reads/coverage?

Hi,

I need to pool 10 multiplexed libraries with different insert sizes (from 245 to 285 bp). Two of the libraries are inputs. The rest are IPs. We ordered 50 million reads for each library, 150...
Forum: Sample Prep / Library Generation 04-09-2019, 07:00 AM
Replies: 18
Views: 1,674
Posted By KB*
Thank you very much, @arctan and @GenoMax for you...

Thank you very much, @arctan and @GenoMax for you help.

I now can only go Novaseq.

I got some more information from the core (below). Could anybody please comment?

1) The core fails...
Forum: Sample Prep / Library Generation 04-09-2019, 03:35 AM
Replies: 1
Views: 486
Posted By KB*
It happens, the discussion continue here ...

It happens, the discussion continue here
http://seqanswers.com/forums/showthread.php?t=88202
Forum: Sample Prep / Library Generation 04-09-2019, 03:29 AM
Replies: 18
Views: 1,674
Posted By KB*
5309 Hi @luc, Than you very much for...

5309

Hi @luc,

Than you very much for your question about sonication. It is a deviation, but I am glad I can share my experience. I hope somebody might find it interesting/useful.

Either...
Forum: Sample Prep / Library Generation 04-09-2019, 03:16 AM
Replies: 4
Views: 1,153
Posted By KB*
I used AmpPure beads ~ + 4 month. They have...

I used AmpPure beads ~ + 4 month. They have worked. I have checked mine first with a not important sample. You can test yours with a DNA ladder. I think it is in general a good idea.
Forum: Sample Prep / Library Generation 04-08-2019, 05:31 AM
Replies: 18
Views: 1,674
Posted By KB*
Dear all, Dear @arctan @GenoMax, please help...

Dear all,

Dear @arctan @GenoMax, please help :-) I am lost.....

I got the answer from the sequencing facility. The libraries were failed because they have "short fragments". They are not...
Forum: Sample Prep / Library Generation 04-04-2019, 07:25 AM
Replies: 18
Views: 1,674
Posted By KB*
Thank you @GenoMax for the suggestion. I guess...

Thank you @GenoMax for the suggestion. I guess with size-selection I can focus on libs 21-27 (libs 15-20 and 21-27 are prepared using different cell lines. So essentially those are the two different...
Forum: Sample Prep / Library Generation 04-04-2019, 05:37 AM
Replies: 18
Views: 1,674
Posted By KB*
Oh, @bman I wish I know the answer. May be...

Oh, @bman
I wish I know the answer. May be check the slide presentation I refer to in my previous answer [2]. I do not know may be you are preping some special kind of libraries. I am peping...
Forum: Sample Prep / Library Generation 04-04-2019, 05:18 AM
Replies: 18
Views: 1,674
Posted By KB*
@arctan, @luc, @bman So happy to hear your...

@arctan, @luc, @bman
So happy to hear your answers and the discussion :)

Sorry for low res images. Prepared the new file with better images (only the seq.facility report. File is attached).
...
Forum: Sample Prep / Library Generation 04-03-2019, 06:46 AM
Replies: 1
Views: 486
Posted By KB*
Why X-ChIP libraries QC failed?

Hi,

Please advise on the quality of the libraries. There are 10 in total (library ID, cell type, IP type)
15 - cell type 1, input;
16 - cell type 1, IP #1;
18 - cell type 1, IP #2;
19 - cell...
Forum: Sample Prep / Library Generation 04-03-2019, 06:10 AM
Replies: 18
Views: 1,674
Posted By KB*
Thank you @arctan for the answer, I actually...

Thank you @arctan for the answer,

I actually ended up doing one more PCR cycle. All but one library (input #15) looked OK for me. I tried to re-size-select #15 ending up with loosing DNA. Anyway,...
Forum: Sample Prep / Library Generation 03-16-2019, 01:27 AM
Replies: 18
Views: 1,674
Posted By KB*
HMW tail in the library. Remove or leave and sequence?

Hi there,
Skipping all the suffering.. I now have my libraries for ChIPs-Seq: good looking peaks, but also a high molecular weight something on the right of the upper marker :eek: Worth to notice,...
Forum: Sample Prep / Library Generation 03-16-2019, 01:00 AM
Replies: 17
Views: 10,321
Posted By KB*
Question also have HMW tail

Hi ssing,
Are you still around? I have samples looking similar to yours (check the image). I am preparing libraries on ChIPed DNA and all my IPs and IgG IPs have this tail. Only input does not have...
Forum: Sample Prep / Library Generation 11-26-2018, 03:19 PM
Replies: 15
Views: 20,350
Posted By KB*
2018 - Large fragments observed as well

Hi, guys.
The same here. I am preparing ChIP-Seq samples for a "co-factor". There is only 1 paper reporting it binds to DNA at all. In a different cell line :D

My IP on well sheared chromatin...
Forum: Introductions 07-03-2018, 09:56 AM
Replies: 0
Views: 858
Posted By KB*
Cool Hi.. oh so many questions...

Hi,
I am new to NGS. Currently trying to prep my DNA for ChIP-Seq. With some success. Yet, did not even get to PCR to validate my targets. But, I got a great idea :D!!! Another researcher already...
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