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Forum: Epigenetics 04-01-2011, 07:54 AM
Replies: 4
Views: 2,310
Posted By NGene
Thanks a lot for the replies. I totally...

Thanks a lot for the replies.

I totally agree that tweaking should be the refining part. However, I think that even though the filtering cuts down lots of the reads, the total read numbers are...
Forum: Epigenetics 02-28-2011, 01:11 AM
Replies: 22
Views: 9,529
Posted By NGene
I would be interested in knowing captainentropy...

I would be interested in knowing captainentropy prep protocol too.

Concerning your protocol, ETHANol, I would be glad to read it too. I am sending a pm with my e-mail, if you do not mind.
Forum: Epigenetics 02-15-2011, 01:22 AM
Replies: 22
Views: 9,529
Posted By NGene
I would exclude large deletions since the genome...

I would exclude large deletions since the genome of the cell line I am using is sequenced and annotated. Besides, I assume I would get no reads if a deletion occurs (in a homogeneous population); I...
Forum: Epigenetics 02-14-2011, 04:10 AM
Replies: 4
Views: 2,310
Posted By NGene
CisGenome Analysis

I could not find any topic committed to such a tool, therefore I decided to open a new one. In case it already exists, feel free to merge.

I am handling some output sequences from Illumina GAII...
Forum: Epigenetics 02-14-2011, 01:56 AM
Replies: 22
Views: 9,529
Posted By NGene
I am aware of regions that are depleted of...

I am aware of regions that are depleted of histone/nucleosomes (especially active promoters, as you say). The point is that I am talking about very big domains (more than 5 Mbp) where the abundance...
Forum: Epigenetics 02-11-2011, 09:21 AM
Replies: 22
Views: 9,529
Posted By NGene
I am facing this issue too. I guess I am...

I am facing this issue too. I guess I am enriching parts of the genome which are less crosslinked, losing likely the heterochromatin (which is what I am interested in...).
I believe that my...
Forum: Epigenetics 02-11-2011, 05:58 AM
Replies: 5
Views: 6,732
Posted By NGene
If you do not want to switch to A protein beads,...

If you do not want to switch to A protein beads, you do not want to use IgG-negative control and you do not want to block the beads, you might want to play with salt concentration and...
Forum: Introductions 02-11-2011, 05:21 AM
Replies: 373
Views: 125,016
Posted By NGene
Greetings! I am a postdoc working in germany...

Greetings!

I am a postdoc working in germany and have just approached the next-gen sequencing technologies. I am performing ChIP-Seq studies by Illumina-Solexa.

I am glad this forum is up.
...
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