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Questions related to Sequencing
Hello, I am preparing RADseq libraries. I am shearing digested DNA (mean size 4096bp) using a Covaris ME220. The shearing is not working as fast as it should (compared to undigested DNA). Does...
16 November 2016 9,451 4 View
Which changes (parameters) can improve CID results?
16 November 2016 853 3 View
How should identify genotype of individuals for an association study? I have got sequence of each individual related to my desired gene and conducted SNP analysis for them, but I don’t know the...
15 November 2016 8,980 3 View
I am completely new in this QIIME's world. I have been trying to analyze my data set, it is composed by 2 samples: Sample 1: V1V2, V3V4, V4V6 16S rRNA amplicon. Sample 2: V3V4 16 So, the data is...
15 November 2016 6,611 4 View
A company is offering 1Gb for $xxx. Since it is supposed that 1Gb=10^9 bases, is it enough for assemble a whole bacterial genome (~9Mb)?
14 November 2016 413 4 View
When I was looking for some information about CCAT1 gene in NONCODE, I realised that some part of sequence is written with capital letters and some part with lowercase letters,...
13 November 2016 5,124 1 View
I have been unable to get useful results from the REGA HIV-1 subtyping tool for the past 48 hours (link below). Although my sequences are uploaded in the FASTA format (less than 10 sequences at a...
11 November 2016 7,529 4 View
I am looking for a protocol or kit for RIP seq in a rare cell population. I am sorting this rare cell population by FACS, but only get around 3K cells per experiment. However, I know that my RBP...
10 November 2016 1,757 1 View
I am looking to do a sister chromatid exchange (SCE) assay to complement some single cell sequencing copy number results but do not have access to a UVA source. I am wondering if hydrogen...
09 November 2016 917 2 View
I would like to do sequencing of a species of Charophyceae, for which, I have collected a few morphologically differing members from different locations. I would like determine if there is any...
08 October 2016 8,198 5 View
BLAST analysis shows 99.7% similarity with a species but morphologically they both have lots of differences !
08 October 2016 6,889 4 View
Sequences of marine invertebrates were run on blast. The attached photo depicts the results. Kindly advice. thank you.
24 August 2016 3,041 2 View
Hi all, As far as I know, TransDecoder, GeneMarkS-T, Prodigal and ESTScan can detect CDSs from assembled sequences. Besides, any others? Thanks.
04 August 2016 10,013 4 View
I was uploading the sequence data to the MG-RAST server, and the notice that sequence stats calculation failed kept popping out when the upload process was about to complete, meanwhile the...
03 August 2016 1,277 4 View
I am trying to amplify an AT rich sequence which is 1543 bp long but still unsuccessful. I have used Phanta Max and Taq enzymes. Please suggest possible solution for it.
07 July 2016 9,158 3 View
I need to identify my fungi, i isolated dna and now which region i will amplify? 18SRNA, 16S RNA or the ITS sequence region?
07 July 2016 2,907 2 View
Hi, I recently upload raw sequence reads to NCBI Sequence Read Archive (SRA). I followed the steps: (1) Make BioProject, (2) Make BioSamples (3) Submit to SRA (Beta) using Aspera Connect. However,...
07 July 2016 2,826 3 View
We used a small amount of our digest (5ul out of 100) and ran on the gel to confirm the digests success, when the rest of the digest sample was quantified with nano drop however, no DNA could be...
07 July 2016 6,435 12 View
For example my 260/280 ratio is 2.08 and my 260/230 ratio is 0.68 measured with nanodrop. Would a bad 260/230 ratio lead to bad sequencing?
07 July 2016 6,172 7 View
Hi, Has anyone used Qiagen's RNeasy 96 Universal tissue kits? How did you find it? Also, what about Macherey Nagel's NucleoSpin™ 96 RNA? Which is better? I have 6000+ bees to homogenate and...
07 July 2016 6,427 2 View
So, I'm about to start this new project and I'm wondering if there are new trending techniques to insert LoxP sites flanking an exon in the mouse genome. We use CrispR/Cas9 system in the lab, so...
28 June 2016 4,873 2 View
I have a 16S rRNA sequence that has 100% of similarity to a bacterial species (Brevibacterium halotolerans ) that is included in a taxonomic group (Bacillus subtilis group). Does that result mean...
22 June 2016 909 8 View
Hi All, My gene is 1248 bp long (that I cloned into a pET-30Xa/LIC vector). I wanted to create a site-directed mutation around 687 bp. I used Agilent's Quik change mutation kit. Reverse sequencing...
06 June 2016 6,544 4 View
I'm planning to repeat MiSeq Illumina run that underclustered. For the beginning, I will increase the load 2-fold to 20 pM. Did anyone tried to add Tris-Cl after denaturation to neutralize NaOH as...
06 June 2016 8,313 7 View