Forum: Bioinformatics
05-06-2020, 11:01 AM
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Replies: 0
Views: 686
Windows Ubuntu, Kallisto, R, sleuth, conda, bioconda, miniconda, bioconductor
Hello everyone,
I'm trying to sort out getting sleuth working with R. I currently have windows ubuntu subshell running and have installed conda, bioconda, bioconductor, R, kallisto, and sleuth....
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Forum: RNA Sequencing
05-16-2019, 08:42 AM
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Replies: 1
Views: 2,961
high percentage of reads mapping to tRNA?
How do you interpret this? What does it mean for wet-lab side of things, does it inform any step that went right or wrong? This is for a total RNAseq minus rRNA experiment....
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Forum: Bioinformatics
12-07-2018, 06:34 AM
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Replies: 1
Views: 1,491
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Forum: Sample Prep / Library Generation
10-26-2018, 06:46 AM
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Replies: 1
Views: 1,762
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Forum: Sample Prep / Library Generation
07-11-2018, 08:04 AM
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Replies: 2
Views: 1,821
hi austinso,
thanks for the information....
hi austinso,
thanks for the information. i'm going to run through the calculations so that i understand the math better. i will have enough for sequencing because i can normalize all of my...
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Forum: Sample Prep / Library Generation
07-10-2018, 09:12 AM
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Replies: 2
Views: 1,821
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Forum: Core Facilities
06-06-2018, 08:25 AM
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Replies: 3
Views: 6,084
pacbio sequel system
how much do core facilities charge to run the instrument, not per sample or SMRTcell but just to recover the cost of running the device? (electricity, nitrogen, etc.)
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Forum: Core Facilities
06-06-2018, 08:11 AM
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Replies: 1
Views: 4,892
yes
we have the same exact problem. its just meant to make more money for agilent sadly. have yet to find a workaround
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Forum: Sample Prep / Library Generation
05-30-2018, 07:06 AM
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Replies: 1
Views: 1,678
Thermal cycler with variable temperature lid?
Does this machine exist:, for example, a machine that can change the lid temperature during the course of the reactions? Something tells me that having the lid set to 75C when my reverse...
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Forum: Sample Prep / Library Generation
05-10-2018, 01:19 PM
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Replies: 6
Views: 3,146
Is Qubit good for multiple samples?
Hello,
We've been having some quantitation issues recently, I'm wondering whether the Qubit fluorometers are good for processing lots of samples (96 at a time?)
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Forum: RNA Sequencing
11-08-2017, 07:36 AM
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Replies: 5
Views: 2,462
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Forum: RNA Sequencing
11-08-2017, 07:23 AM
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Replies: 5
Views: 2,462
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Forum: Introductions
10-16-2017, 07:14 AM
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Replies: 3
Views: 1,134
concentrating DNA
Do a concentration and purification using AMPure XP magnetic beads (they are SPRI beads, you can google how they work if interested) and concentrate and purify the DNA using these and a magnetic...
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Forum: Sample Prep / Library Generation
10-11-2017, 05:57 AM
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Replies: 4
Views: 3,450
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Forum: RNA Sequencing
10-09-2017, 01:26 PM
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Replies: 2
Views: 1,514
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Forum: Sample Prep / Library Generation
08-24-2017, 11:49 AM
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Replies: 2
Views: 3,442
troubleshooting agilent bioanalyzer error
I ran an RNA 6000 nano chip with RNA samples in all 12 wells, some randomly came back flagged with error: unexpected signal in fast region. Is there any way to troubleshoot this after the fact to get...
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Forum: Sample Prep / Library Generation
08-14-2017, 09:12 AM
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Replies: 7
Views: 3,388
electropherogram error
Hello,
trying to be of some assistance here, what were your errors? If you look on the simulated gel to the right there is a red dot, which indicates an error has occurred, whether some peak on...
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Forum: Sample Prep / Library Generation
08-09-2017, 05:59 AM
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Replies: 0
Views: 1,145
Low input of primers for pre optimized PCR step
Hello,
I have created a situation where I only have enough reagents to add approximately 1/5 of the primers recommended (pre optimized by Illumina) for a library amplification step (to each well...
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Forum: Pacific Biosciences
05-26-2017, 07:30 AM
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Replies: 2
Views: 3,030
bluepippin size selection for SMRTbells
Hello,
at which step of the 10kb protocol for preparation of SMRTbell libraries do you run BluePippin 20kb cassette for size selection? I am preparing gDNAs for complete sequencing.
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Forum: Pacific Biosciences
05-22-2017, 11:45 AM
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Replies: 2
Views: 2,940
PacBio reagents
If a box of PacBio polymerase binding reagents is left at room temperature and allowed to warm to ambient temperature is it now useless?
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