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Questions related to Sequencing
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 7,456 2 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 2,409 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 2,120 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 8,639 2 View
I need that file of rCRS to use it in BioEdit (Sequence Alignment Editor). I know the rCRS exists...
12 August 2018 1,181 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 8,647 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 3,260 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 4,754 4 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 7,511 6 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 2,926 3 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 1,856 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 7,347 4 View
Hello everyone, I am trying to construct a plasmid vector with two promoters in opposite direction (one in clockwise and other in anticlockwise direction on circular map). Should I add spacer...
29 July 2017 8,037 3 View
I have to analyze PacBio transcriptome data with four bin sizes: 1-2 Kb, 2-3 Kb, 3-6 Kb and 5-10 Kb. I can understand that the HSP length cut-off and HSP-Hit coverage settings must be customized...
27 July 2017 1,449 1 View
Can anyone recommend software for the design of an sgRNA for use in Staphylococcus aureus with the CRISR system? I have tried other systems, but I would like the system to look for possible off...
26 July 2017 3,081 1 View
I plan to carry out sequencing of a bacterial integron using random primer walking to identify the structure of internal genes.Is there a program on ncbi homepage that can draw graphics of gene...
24 July 2017 6,346 3 View
We want to sequence RNA from passerine bird blood to look at host expression. We will need to remove the ribosomal RNA and also the globin RNAs during the library preparation. There is no...
17 July 2017 1,908 4 View
Best software for amplicon seq data analysis for malaria parasite. EditI know that there are many software (QIIME,mothur, and others ) to analysis amplicon sequence data for microbial (SPECIALLY...
15 July 2017 4,721 2 View
I need a frequently curated database of Bacterial Insertion sequences which can be downloaded and used as input for standalone local BLAST to ascertain the presence of Insertion sequences in the...
14 July 2017 6,241 1 View
I am trying to figure out how far the promoter/regulatory region of the immunoglobulin variable regions stretches upstream of the startcodon. I am aware that the conserved octamer sequence...
13 July 2017 4,531 2 View
Dear all, I want check the similarity of a list of genes' 5′-UTR regions across different species. Anybody could recommend me to do it in an efficient way, please? Best, Bochao
12 July 2017 5,680 1 View
Hello everyone, Does anyone has primers squances for hpv? and what is the tool to detect their visability? I searched different primers squances using NCBI but non matched the primer sequance I...
10 July 2017 3,424 3 View
There are some >150 types of HPV (human papilloma viruses); I am looking for the conserved regions from their genome.
08 July 2017 868 3 View
I have got a sequence from company as I did colony PCR using 16S primers. Now my question, can I make a phylogentic tree using that sequence?? If yes how? Explain. Thanks
08 July 2017 5,382 4 View