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Forum: Sample Prep / Library Generation 09-01-2017, 04:56 AM
Replies: 1
Views: 4,053
Posted By vadoue
Hi you! I was wondering if you got your...

Hi you!

I was wondering if you got your answer. Also I saw that you used HiSeq3000. Did you used 2x75 or 2x150bp reads? I am planning to use 2x150 and I was wondering if I could "lost" small...
Forum: Bioinformatics 09-01-2017, 04:49 AM
Replies: 3
Views: 2,917
Posted By vadoue
Is it OK to use paired-end 150bp to sequence ATAC-seq libraries?

Hi!

I am planning to do ATAC-seq assays and I am wondering if it is fine to use paired-end 150bp to sequence ATAC-seq libraries? :confused:
Just because the sequencing platform I am working with...
Forum: Sample Prep / Library Generation 09-09-2015, 01:22 AM
Replies: 2
Views: 1,693
Posted By vadoue
No idea? :(

No idea? :(
Forum: Sample Prep / Library Generation 09-03-2015, 04:08 AM
Replies: 2
Views: 1,693
Posted By vadoue
Single cell RNA-seq with FFPE samples?

Hi!!

I would like to sequence mRNA from about 200 nucleus of FFPE samples. So it is not exactly single cells but as it is only the nucleus I will have very little mRNA at the end...

I know...
Forum: Sample Prep / Library Generation 04-28-2015, 12:40 AM
Replies: 5
Views: 1,780
Posted By vadoue
The problem came from the library prep. I was...

The problem came from the library prep. I was doing the PCR after size selection on agarose gel. The problem was that as I had to cut without seeing any band I was selectionning few DNA which was...
Forum: Sample Prep / Library Generation 04-28-2015, 12:34 AM
Replies: 11
Views: 4,041
Posted By vadoue
As it is a rare cell type I don't know any...

As it is a rare cell type I don't know any control loci. But ChIP-qPCR data on potential loci had always been bad with this antibody... I will try a new aliquot. Would you have any explanation of...
Forum: Sample Prep / Library Generation 04-27-2015, 08:08 AM
Replies: 11
Views: 4,041
Posted By vadoue
Hi! Thanks for your answer!! As I have...

Hi!

Thanks for your answer!!

As I have no peaks only with this antibody, I am wondering if the problem could come from the antibody itself as it has been store for more than one month at 4...
Forum: Sample Prep / Library Generation 04-14-2015, 05:20 AM
Replies: 11
Views: 4,041
Posted By vadoue
Hi dv88! I would be interested to know if...

Hi dv88!

I would be interested to know if your H3K9ac ChIP finally worked I have the same issue (my ChIP-seq data show no peaks for this histone mark whereas I can see nice peaks with others...
Forum: Sample Prep / Library Generation 11-12-2014, 04:21 AM
Replies: 12
Views: 7,769
Posted By vadoue
Hi, Did anyone find a solution for this...

Hi,

Did anyone find a solution for this issue??

Thanks!
Forum: Sample Prep / Library Generation 11-07-2014, 02:54 AM
Replies: 5
Views: 1,780
Posted By vadoue
Thanks for your answer! :) You can find...

Thanks for your answer! :)

You can find attached the sonication profiles for some of the samples (some too concentrated...) as well as the libraries profiles.

I used a Qubit for quantification...
Forum: Sample Prep / Library Generation 11-06-2014, 10:24 AM
Replies: 5
Views: 1,780
Posted By vadoue
High duplicates in ChIP samples (lib prep issue?)

Hi,

I am working with ChIP-seq data with enrichment close to background. Only sample for the histone mark H3K4me3 look fine with well defined peaks. The others samples (H3K9me3/ac) are really bad...
Forum: Bioinformatics 11-06-2014, 06:58 AM
Replies: 0
Views: 1,144
Posted By vadoue
High duplication rate for INPUT (ChIP-seq)

Hi all,

I am analysing ChIP-seq data and got very noisy output except for the histone mark H3K4me3. The others marks (H3K9me3 and H3K9ac) and particularly the input samples got high rate of...
Forum: Sample Prep / Library Generation 11-06-2014, 06:47 AM
Replies: 1
Views: 2,194
Posted By vadoue
Hi Brian, Did you figure out what happened??...

Hi Brian,

Did you figure out what happened??

I have the same kind of problem...

Thanks! :)
Forum: Bioinformatics 11-04-2014, 05:40 AM
Replies: 2
Views: 877
Posted By vadoue
It seems to be a bwa version or compilation...

It seems to be a bwa version or compilation issue... I used same command but with full path to bwa (bwa-0.7.10) and now it is working.

Thanks!
Forum: Bioinformatics 11-04-2014, 04:22 AM
Replies: 2
Views: 877
Posted By vadoue
BWA exit issue

Hi guys! :D

I am having troubles running BWA with ChIP-seq paired-end data (100bp from HiSeq2500).

It stop suddently without any specific error message. What is even more strange is that when I...
Forum: Sample Prep / Library Generation 07-04-2014, 02:55 AM
Replies: 3
Views: 1,267
Posted By vadoue
It seems that a second Ampure purification step...

It seems that a second Ampure purification step (1:1) worked for me to removed most primer-dimers. You should use less adaptors in your protocol. In your bioanalyser profile, the contamination is so...
Forum: Sample Prep / Library Generation 07-03-2014, 12:08 AM
Replies: 3
Views: 1,267
Posted By vadoue
Hi, I am happy to read you since I have...

Hi,

I am happy to read you since I have exactly the same problem... I used others library kits before and I never got any primer-dimer contamination. This time I used ScriptSeq and I have an extra...
Forum: Bioinformatics 01-17-2013, 06:39 AM
Replies: 1
Views: 940
Posted By vadoue
Identification of Transcription factor using Matrix

Hi,
I have a list of SNPs for which I would like to identified sites for transcription factor binding (using sequence around). I would like to use known motifs (for ex from TRANSFAC database) as...
Forum: RNA Sequencing 11-19-2012, 07:38 AM
Replies: 0
Views: 1,562
Posted By vadoue
FKPM normalization: how to deal with cell type purity?

Hi all,
I hope that you can help me... I am working with some blood purified cells from different individuals and different time-points. My problem is that when I want to look at which genes are...
Forum: Bioinformatics 11-19-2012, 07:36 AM
Replies: 0
Views: 945
Posted By vadoue
FKPM normalization: how to deal with cell type purity?

Hi all,
I hope that you can help me... I am working with some blood purified cells from different individuals and different time-points. My problem is that when I want to look at which genes are...
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