Forum: Illumina/Solexa
04-26-2015, 06:47 PM
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Replies: 6
Views: 2,212
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Forum: Bioinformatics
06-18-2014, 09:12 PM
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Replies: 0
Views: 1,850
multiple multiWig files for UCSC
There are some good examples on how to make a single multiWig file for visualization with a UCSC track hub, but I have 48 multiWig's I would like to make (i.e. 48 tracks from 288 wig files). Does...
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Forum: RNA Sequencing
02-17-2014, 04:41 PM
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Replies: 0
Views: 1,586
Multi-mapped reads - Lior Pachter
I was watching this video of Lior Pachter at CSHL last year and he's talking about what to do with multi-mapped reads and it makes no sense to me. What I think he is saying is that by assigning...
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Forum: Illumina/Solexa
09-08-2013, 07:04 PM
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Replies: 1
Views: 3,643
Off-line Basecaller (OLB) not demultiplexing
We (I) screwed up and lost the control lane from a run. The other lanes are methylC-seq libraries so they cannot be used for the control lane so we wanted to run Illumina's Off-line Basecaller (OLB)...
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Forum: Illumina/Solexa
06-21-2013, 02:00 AM
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Replies: 75
Views: 37,632
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Forum: Sample Prep / Library Generation
06-07-2013, 03:29 AM
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Replies: 2
Views: 1,988
SPRI beads (AMPure) work on any nucleic acid,...
SPRI beads (AMPure) work on any nucleic acid, dsDNA, ssDNA, RNA, DNA/RNA hybrid. The higher the PEG/NaCl concentration the smaller the fragments you recover, albeit the secondary structure of single...
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Forum: Sample Prep / Library Generation
06-04-2013, 04:27 PM
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Replies: 35
Views: 24,872
The original dUTP protocol required massive...
The original dUTP protocol required massive amounts of starting material because the ActD. If you removed ActD from the protocol you still got pretty good strandedness but required a lot less...
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Forum: Sample Prep / Library Generation
05-30-2013, 12:22 AM
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Replies: 35
Views: 24,872
Not sure what that means so....
From the...
Not sure what that means so....
From the Illumina website.
/truseq_stranded_mrna_lt_sample_prep_kit/questions.ilmn
How is strandedness maintained after DNA amplification?
Strandedness is...
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Forum: Epigenetics
05-26-2013, 11:39 PM
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Replies: 58
Views: 49,159
Wordpress.com has some problems. If you just...
Wordpress.com has some problems. If you just keep clicking reload a bunch of times it will eventually load. Annoying and I'd like to move my blog somewhere more reliable but it never makes it up to...
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Forum: Illumina/Solexa
11-26-2012, 05:05 AM
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Replies: 2
Views: 3,000
This is not your problem. It's something more...
This is not your problem. It's something more serious but you should use the KAPA HF polymerase. It is way better with GC-rich templates then the TruSeq polymerase and way better in general.
As...
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Forum: Bioinformatics
11-09-2012, 07:18 PM
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Replies: 9
Views: 8,196
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Forum: Sample Prep / Library Generation
10-29-2012, 09:53 PM
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Replies: 9
Views: 5,856
If you are doing acoustic shearing you can get...
If you are doing acoustic shearing you can get away with skipping the gel extraction and use AMPure to get rid of adapter-dimer. If you are using mononucleosomal DNA, in my experience you should do,...
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Forum: Bioinformatics
10-17-2012, 05:46 PM
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Replies: 9
Views: 8,196
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Forum: Sample Prep / Library Generation
10-17-2012, 03:31 PM
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Replies: 14
Views: 11,116
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Forum: RNA Sequencing
10-16-2012, 04:26 AM
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Replies: 7
Views: 5,154
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Forum: Bioinformatics
09-22-2012, 07:07 PM
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Replies: 23
Views: 44,077
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Forum: RNA Sequencing
09-13-2012, 10:11 PM
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Replies: 5
Views: 2,359
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Forum: Epigenetics
09-10-2012, 01:03 AM
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Replies: 6
Views: 5,031
I'll be the third to basically say the same...
I'll be the third to basically say the same thing. In my experience MeDIP-seq data is really messy and can be a bit hard to interpret. Not impossible but the data analysis probably going to be...
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Forum: Bioinformatics
09-02-2012, 03:01 AM
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Replies: 11
Views: 3,520
You'll never be able tell which gene are truly...
You'll never be able tell which gene are truly not expressed. That's how science works. We can only see what is, you can never see what isn't!!!!!
In this case you will always be able to say, if...
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Forum: Bioinformatics
09-02-2012, 02:57 AM
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Replies: 9
Views: 2,981
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Forum: Bioinformatics
09-01-2012, 06:26 AM
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Replies: 1
Views: 4,229
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Forum: Bioinformatics
08-31-2012, 05:31 AM
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Replies: 9
Views: 2,981
Or you could run this R script to merge your...
Or you could run this R script to merge your HTSeq-count output files. Probably a little quicker then Excel if you have a lot of files. Anybody know how to do this with a BASH script??
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Forum: Epigenetics
08-09-2012, 11:47 PM
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Replies: 2
Views: 5,795
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Forum: Epigenetics
08-05-2012, 12:55 AM
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Replies: 58
Views: 49,159
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Forum: RNA Sequencing
07-11-2012, 12:00 PM
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Replies: 21
Views: 12,653
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