Forum: Illumina/Solexa
08-04-2015, 12:38 AM
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Replies: 9
Views: 9,297
I emailed Illumina's representatives here in...
I emailed Illumina's representatives here in Israel but didn't get an answer. I think that the explanation I gave above is reasonable (maybe low efficiency of RT in the cluster?). With v.2 chemistry...
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Forum: Illumina/Solexa
02-23-2015, 02:52 AM
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Replies: 2
Views: 3,103
I didn't try to contact them yet, I'm trying to...
I didn't try to contact them yet, I'm trying to see if it's common or related to the library construction first. The libraries have a 9 bp barcode and they are bacterial rRNA depleted transcriptomes...
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Forum: Illumina/Solexa
02-22-2015, 07:32 AM
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Replies: 2
Views: 3,103
Nextseq500 N's from position 25
Hi,
I've been seeing a lot of Nextseq500 runs lately and I found a very disturbing phenomenon. In a lot of the runs I start seeing a lot of N's from cycle 25 onward. The FastQC looks like this:...
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Forum: Sample Prep / Library Generation
12-25-2014, 01:02 AM
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Replies: 68
Views: 26,142
Some insights from our test nextseq run.
We...
Some insights from our test nextseq run.
We took some RNA (8 RNAseq libraries), prepared the libraries after RiboZero, fragmentation and size selection. The process was indeed shorter (1.5 days) and...
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Forum: Bioinformatics
12-21-2014, 05:52 AM
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Replies: 4
Views: 1,871
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Forum: Bioinformatics
12-18-2014, 05:39 AM
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Replies: 4
Views: 1,871
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Forum: Bioinformatics
12-18-2014, 03:08 AM
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Replies: 4
Views: 1,871
DESeq2 LRT insights
Hi,
We're working on a RNA binding protein and want to figure out if it binds different RNAs in 2 different conditions. We did an immunoprecipitation (IP) for the protein and prepared the RNA that...
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Forum: Sample Prep / Library Generation
12-14-2014, 12:34 AM
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Replies: 4
Views: 2,797
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Forum: Illumina/Solexa
12-10-2014, 10:18 PM
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Replies: 3
Views: 2,083
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Forum: General
12-10-2014, 03:51 AM
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Replies: 16
Views: 4,296
I opened Lehninger (Principles of biochemistry,...
I opened Lehninger (Principles of biochemistry, 4th ed.) on page 293. I quote:
C is deaminated to U in a rate of 10^-7 in 24 hours, which means 100 mutations a day for a mammalian cell which would...
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Forum: Introductions
12-09-2014, 05:34 AM
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Replies: 8
Views: 2,263
We got an offer from SQREAM...
We got an offer from SQREAM (http://www.sqreamtech.com/), they develop a fast GPU based SQL server with the storage of infinidat (http://www.infinidat.com/).
They have a niche for biological data...
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Forum: RNA Sequencing
12-09-2014, 05:26 AM
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Replies: 1
Views: 2,364
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Forum: Bioinformatics
11-19-2014, 11:37 PM
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Replies: 2
Views: 1,113
Look at iTOL help page under "Uploading and...
Look at iTOL help page under "Uploading and working with your own trees" to display bars. I think the only way to mark a group is by coloring it. After you upload the tree click on "Define color...
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Forum: Sample Prep / Library Generation
11-18-2014, 01:15 AM
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Replies: 68
Views: 26,142
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Forum: Sample Prep / Library Generation
11-16-2014, 01:53 PM
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Replies: 68
Views: 26,142
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Forum: RNA Sequencing
11-01-2014, 12:51 PM
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Replies: 5
Views: 1,705
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Forum: RNA Sequencing
10-30-2014, 12:16 AM
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Replies: 5
Views: 1,705
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Forum: RNA Sequencing
10-07-2014, 03:20 AM
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Replies: 3
Views: 1,368
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Forum: RNA Sequencing
10-06-2014, 01:32 AM
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Replies: 6
Views: 2,177
Maybe you should compare pairs
You're going to stumble into many normalization issues here. I'm having trouble comparing experiments from the same lab in two different experimental settings, let alone different labs and bacteria....
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Forum: Illumina/Solexa
07-20-2014, 11:28 AM
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Replies: 9
Views: 9,297
poly-G in NextSeq
Hi,
I just received NextSeq paired-end results (45 bp 1st read and 40 bp second read) and I noticed (using fastQC) that about 1-2% of the second read is poly-G. I known that G has no "color" so it...
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