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Questions related to Sequencing
I followed a regular CRISPR-cas9 transfection protocol, manually picked colonies into a 96-well plate and performed nested PCR which I then sent in for sequencing. In my previous 3 runs, I have...
12 July 2019 3,016 4 View
When we amplify 16S rDNA for sequencing using degenerate primers the amplified gene will result to amplicons with different sequences even with the same DNA band size. I assume that it will be...
28 March 2019 2,915 3 View
I am working with DNA methylation currently. I am creating hypomethylation condition in the cells. so how to confirm that the hypomethylation has occurred. sequencing of only LINE-1 gene will be...
20 March 2019 3,435 1 View
I've been using BioEdit for a decade but since it has no support and more like abandonware now I'd like to switch to a new sequence editing software which is being actively maintained. I would...
04 February 2019 7,550 6 View
Has any one applied or can help me in understanding the inductive inference algorithm for partial discharges pattern recognition.
21 January 2019 1,414 1 View
I have mRNA sequence, from which i need to clip the UMI tag. Kindly suggest.
21 December 2018 1,289 2 View
Hi, everyone, I sequenced some samples in the Illumina MiSeq, got the results but now I don't know how to analyze them. I already read the User guide from Illumina, but it's only about the...
03 December 2018 9,643 3 View
If you were a researcher interested in investigating a particular group of prokaryotes (e.g. Cyanobacteria) from an environmental sequencing project, which of the following approaches to taxonomy...
27 October 2018 7,264 3 View
EDIT 29/10/2018: Added more details to bottom. This might be a bit weird, but I thought I'd try here anyway. Is it possible to configure Bowtie2, or similar programs, to match my query-sequence...
25 October 2018 7,571 2 View
I want to submit complete chloroplast genome into NCBI. The genes with intron/introns show problem. The NCBI give the error that gene contains stop codon. I don't understad, how to define the CDS...
11 October 2018 8,256 0 View
Dear all, Recently I saw a paper where cases and controls differed at the sequencing depth. I wonder if this indicates a systematic bias, or it may be due to biological variation. I will be more...
17 September 2018 2,492 2 View
I am a student currently working on a project that requires the sequencing of DNA from two species of California sunflowers. For the record I am using the ddRADseq method. Although I am familiar...
28 August 2018 2,233 7 View
Hello, I have sequencing data of cattle blood plasma and data was BLAST with nr/nt database. In resulting file i counted the number of sequence present in different genus. Further selected three...
18 August 2018 8,727 2 View
I need that file of rCRS to use it in BioEdit (Sequence Alignment Editor). I know the rCRS exists...
12 August 2018 1,314 4 View
Hello, I have two cells lines: A375 and Mel-ST. This last one is an immortalized cell line from primary melanocytes. The BRAF gene should be mutated with V600E mutation in A375 cells but not in...
22 June 2018 8,802 6 View
In which phase [Initiation, Planning/Design Phase, Execution and Closing] of a project, project appraisal is conducted to accept or reject a project?
29 March 2018 3,374 9 View
I’m working with high polymorphic target genes and I need as much accuracy as possible to be able to create my own references. If I want to use 1D2 reads, will be Albacore the only software...
16 March 2018 4,904 4 View
Some microsatellite markers found expect size bp of resulting band at gene bank while some not found. How do I know the expect size bp of the resulting band using a microsatellite marker?
11 March 2018 6,754 8 View
Hello, we are currently genotyping chironomids using the classic Folmer LCO1490 and HCO2198 primers. the LCO primer always performs very good, but the HCO primers do mostly bad. We are cycle...
15 December 2017 7,724 6 View
I have some gene sequences. I need to get accession number from NCBI but expert advice to provide CDS. And also said those sequences contain mixture of plus/minus stands, and internal stop codon....
16 November 2017 4,203 0 View
We are planning to open a research facility that will deal with diagnostic and research projects. The Ion Torrent PGM looks like a good option according to price/performance ratio. Feel free to...
15 November 2017 3,003 3 View
09 November 2017 4,988 0 View
Hello, I am sequencing a library for targeted sequencing of CFTR composed by 68 amplicons. The library preparation cames always very well. However, when I sequence at 10pM I get a cluster of...
07 November 2017 1,970 2 View
The project that I am doing now requires me to filter of hg19 sequences from my data set. I have trimmed my read lengths to 50 bp with Qphred = 20. Next, I will be using bowtie2 to align the...
02 October 2017 7,435 4 View