Sequencing

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Questions related to Sequencing

Can someone explain me the purpose of the 3' part of the nextera adaptor sequence (AGATGTGTATAAGAGACAG)?

Hi everyone! I am using a 2-step targeted amplicon approach for my Illumina library preparation and I wonder what's the purpose of the second part of the Nextera adaptors? The entire sequences...

11 May 2017 8,326 6 View

What is the sum of sequence of any differentable function- f(n) ?

(1) How can we find the partial sum of n1000 instantly ? (2) is there is a simple method to find partial sum of the sequence f(n) ? (3) Any general method to compute...

07 May 2017 7,495 3 View

How to detect a conserved region in a particular genus for which a genus specific primer can be designed?

I want to design a single primer pair for a particular genus, involving its 5 species, so that while performing PCR, we involve a single primer pair, instead of 6 primer pairs.

06 May 2017 8,851 2 View

How to exclude PCR duplicates in ddRAD?

Hello, I am trying to find the best way to deal with PCR duplicates in ddRAD data. I was wondering if there is a reliable way to identify and exclude them in a dataset that has been produced...

02 May 2017 10,064 3 View

For sequences u= (u_m), v=( v_m), define the sequence w by w_j= \sum_{m≥0} u_m _{m+j}. Let 0<p<1. If u belongs to l_1 and v to l_p, does w belong l_p?

In case p≥1, it is a classical result on convolution (discrete Young inequality)

01 May 2017 1,069 1 View

How to Organize RNA-Seq fastq data?

Our lab has sent rat cardiac tissue for sequencing and have obtained indigestible fastq data files. Is there a software I can use to organize these fastq sequence files in order to...

28 April 2017 7,954 3 View

For the pople who used reporter vectors to detect CRISPR cas9 indels and mutations: How big the target site did you use?

Is size of over 400bp too big?

27 April 2017 3,707 2 View

Can you suggest me why we remove stop codon when protein sequence is to be analysed and classified in Interpro?

Hello dear friends Can anyone suggest me, please , why we remove stop codon when protein sequence is to be analyzed and classified in Interpro? When i search the sequence with stop codon i m...

27 April 2017 4,178 2 View

How to design primers for Agilent miRNA qPCR analysis?

Helle!I need to verify my miRNA microarray results with qPCR, and I have Agilent kit for RT-qPCR miRNA 1st-strand cDNA synthesis kit (#600036) and miRNA qPCR kit (#600583). It has some kind of...

26 April 2017 5,815 1 View

Are there companys that offer full plasmid sequencing via Next-Generation-Sequencing at competitive prices?

Hi, just want to know your experiences. Gene synthesis companies and also addgene start to use NGS for sequence validation. thus it seems that prices may have dropped to a degree where it becomes...

20 April 2017 2,363 6 View

Is it possible to overlay features in SerialCloner?

Is there a way to annotate features in Serial Cloner that share sequence, such as a primer and a fragment of inserted genomic DNA carrying a CDS? This is possible in MapDraw (Lasergene), but...

20 April 2017 6,159 1 View

Is there any new and reliable mini sequencer that is recommended?

Hi all, Is there any new and reliable mini sequencer that is recommended?

17 April 2017 2,951 3 View

Can multiple assembly with different platforms be used simultaneously for analysis in RNA Seq experiment ?

we have performed assembly using both CLC work bench (average length: 674 bp; N50: 890 bp) and TRINITY (average length: 725 bp; N50: 928 bp) and performed the analysis from both of them...

17 April 2017 6,963 4 View

Is it normal to have a second peak in chromatograms?

I'm seeing a second call inside most peaks of my DNA sequencing data. This second (smaller) peak is exactly the next base called. Has any one seen this before? Is this a problem with primers? I'm...

17 April 2017 7,449 11 View

How to correct N stretches from an assembled NGS contig file?

Hi there, I have recently assembled a NGS HiSeq data with ABySS 2.02. With the default setting (K-mers=64) I had a 183nt stretch of N (or Gap). I have changed k-mer to 40 and the gap reduced to...

15 April 2017 1,050 3 View

How to remove phage DNA from plasmid.

can anyone plese let me know how to clean phage contaminated plasmid.

12 April 2017 4,011 4 View

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09 April 2017 8,861 1 View

Dear All....is it possible to identify the species by sequencing the cDNA (converted from mRNA) with the same primer designed for DNA sequencing??

Dear All, I have little doubt. Normally for the species level identification we all will under go for the DNA Sequencing using designed Primer....is it possible to identify the species by...

06 April 2017 1,819 5 View

Which are the software for primer designing?

I want to amplify mer genes from bacteria. Can you suggest any primer or software for primer designing?

06 April 2017 219 7 View

How is it possible a point mutation to become homozygous from Forwarding primer while being Heterozygous from the Reverse primer?

In Sanger sequencing, what are the possible reasons a particular point mutation to become homozygous from the Forward primer while being the same mutational point a heterozygous in the...

04 April 2017 3,358 3 View

Can sequences of D-Loop mitochondrial DNA from various individuals in a species using different primers used for phylogentic studies?

There are different primers used in sequencing of D Loop region of mitochondrial DNA in horse. Will different primers not result in different sequences? and Can the sequences obtained using...

30 March 2017 6,300 6 View

What is a good website to download plasmid vector maps?

I'll be using pET-44a and I can't seem to find a download of just the vector sequence (preferably with annotations :D). I'm working with CLC and Serial Cloner. I've tried...

28 March 2017 5,245 2 View

For Chip-seq, how to design primers for qPCR validation of purified DNA after imunoprecipation?

I am new to Chip-seq. Currently I am working on a bacterial transcriptional regulator. We do have a few putative binding target genes for the regulator. So I wanted to use qPCR to evalutate the...

27 March 2017 1,652 3 View

How much does it cost to sequence a cyanobacterial (bacterial) genome?

I mean sequencing + assembling. The genome of that species has been already sequenced.

24 March 2017 5,377 3 View

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