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Forum: Bioinformatics 06-04-2014, 03:08 PM
Replies: 5
Views: 5,125
Posted By dbrg77
Try change the order of the option -S to the end,...

Try change the order of the option -S to the end, immediately before your sam file name, i.e.

do the following:
Forum: Epigenetics 03-20-2014, 08:58 AM
Replies: 8
Views: 11,724
Posted By dbrg77
It is better to include input for every chip you...

It is better to include input for every chip you do so that you keep everything in parallel.

Having said that, we have found that peak calling results have negligible differences using different...
Forum: Illumina/Solexa 03-20-2014, 08:51 AM
Replies: 14
Views: 13,877
Posted By dbrg77
check this analysis guide from Illumina, it...

check this analysis guide from Illumina, it should be
fr-unstranded for Trueseq regular
fr-firststrand for Trueseq stranded
...
Forum: Epigenetics 03-05-2014, 07:09 AM
Replies: 2
Views: 6,344
Posted By dbrg77
Thank you for the reply. For some factors, we...

Thank you for the reply. For some factors, we observed exactly what you said. However, we just cannot chip some other factors. Recently, I run my time-course sonication samples on a western blot...
Forum: Epigenetics 02-28-2014, 01:53 PM
Replies: 2
Views: 6,344
Posted By dbrg77
Anyone using Bioruptor Pico?

Hi,

I'm wondering whether anyone here has ever succeeded using Bioruptor Pico sonicator for transcription factor ChIP-qPCR.

Before, we had an old standard Bioruptor which worked okay with both...
Forum: General 03-24-2011, 02:49 PM
Replies: 1
Views: 2,339
Posted By dbrg77
Why using short reads?

Hi, everyone. I'm a newbie here.

I have a question that always baffles me that why NGS only uses short sequence tags?

Instead sequence the whole DNA fragments, it only sequences the first 25-50...
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