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Forum: Sample Prep / Library Generation 11-14-2014, 07:16 AM
Replies: 9
Views: 5,684
Posted By obischof
We did; always smear no matter how long or short...

We did; always smear no matter how long or short you incubate.
Forum: Sample Prep / Library Generation 11-13-2014, 01:19 PM
Replies: 9
Views: 5,684
Posted By obischof
Very much depends on your PCR machine but we have...

Very much depends on your PCR machine but we have similar data. On another note, if you put your amplified material on a gel or bioanalyzer do you observe a nuclesome-like pattern or rather a smear?...
Forum: Sample Prep / Library Generation 11-13-2014, 01:13 PM
Replies: 3
Views: 4,399
Posted By obischof
Has any of you two tried ATACseq yet and if yes...

Has any of you two tried ATACseq yet and if yes do you see a nucleosomal-like pattern after tagmantation? In our hands we only see a smear.
Forum: Sample Prep / Library Generation 10-22-2014, 12:15 PM
Replies: 69
Views: 50,644
Posted By obischof
Duplicate reads in ATACseq

We have run ATACseq on HDFs (100.000 cells) and after paired-end seq on HiSeq2000 (fast run) we get loads of duplicate reads; in fact we loose between 50-90% from the raw reads. Anybody experienced...
Forum: Bioinformatics 06-20-2011, 04:13 AM
Replies: 11
Views: 2,223
Posted By obischof
I will do this asap. What does -m50 actually...

I will do this asap. What does -m50 actually mean?? Would it not be better to run also with the -v parameter set eg at 2?
Forum: Bioinformatics 06-20-2011, 02:30 AM
Replies: 11
Views: 2,223
Posted By obischof
Our bowtie settings were as follows: -a...

Our bowtie settings were as follows:

-a --best -q -m50 -e50 -solexa1.3-quals

We used a control input as reference and qPCRs performed on ChIP samples were all satisfactory for pos and neg...
Forum: Bioinformatics 06-20-2011, 02:29 AM
Replies: 11
Views: 2,223
Posted By obischof
Our bowtie settings were as follows: -a...

Our bowtie settings were as follows:

-a --best -q -m50 -e50 -solexa1.3-quals

We used a control input as reference and qPCRs performed on ChIP samples were all satisfactory for pos and neg...
Forum: Bioinformatics 06-18-2011, 08:47 AM
Replies: 11
Views: 2,223
Posted By obischof
Identical ChIP Seq pattern for different histone abs

We have performed ChIP-Seq using antibodies directed against different histone modfications. After bowtie and MACS14 treatment we find that all peaks fall into repeat regions. Worse, all abs give...
Forum: Sample Prep / Library Generation 01-11-2011, 07:15 AM
Replies: 5
Views: 4,594
Posted By obischof
We had no clusters that passed the internal QC of...

We had no clusters that passed the internal QC of GA, though the first cycle was OK.
Forum: Sample Prep / Library Generation 01-06-2011, 07:50 AM
Replies: 5
Views: 4,594
Posted By obischof
how could that be? what would that explain? Could...

how could that be? what would that explain? Could we still build a library from that?
Forum: Sample Prep / Library Generation 01-06-2011, 07:26 AM
Replies: 5
Views: 4,594
Posted By obischof
Unhappy Agilent Bioanalyzer 2100 detects no DNA

Dear All,

I have run into a huge problem with our seq platform. The problem is as follows. We have prepared chromatin using Mn digestion after PFA XL. We verified the appearance of primarily...
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