Mehrdad Rabiei

13 Questions 27 Answers 0 Followers

Questions related from Mehrdad Rabiei

How to solve a problem in SRA (NCBI)?

Hi all, I have uploaded my all data (DNA and RNA sequences) in SRA. After publishing the data, I suddenly found out some data have not been released and they have been marked "Unaccessioned"! I...

05 January 2023 4,594 1 View

Certain Base/Nucleotide Position in a Primer Pair in PCR Product.

Hi all, Hope you are safe and sound. I have a question for you regarding nucleotide number positions of the two primers (R and F) on the PCR product. I example F-926 /R-1392 universal 16s primer...

01 January 1970 1,665 13 View

Overlapping in forward and reverse reads

I have two forward and reverse reads from HiSeq Illumina platform. The PCR amplicon was 480 bp, 2*240. In merging, how will they have overlapping while they have no common bases? I am just...

01 January 1970 6,853 5 View

Does gDNA co-extract with Plasmid, and vice versa?

For the first time, I am going to extract plasmid. I would like to know whether gDNA would be extracted during the plasmid extracting? Similarly, is the plasmid extracted when gDNA getting to be...

01 January 1970 6,313 3 View

How long does it take to analyze and interpret shotgun metagenomics data?

please reply to me regarding this question. Best regards,

01 January 1970 402 4 View

Three negative controls in qPCR assay

I got confused between two negative controls: NTC (No Template Control) and NC (Negative Control). Am I right? NTC: No DNA or nuclease-free water as a template? NC: Added nuclease-free water as...

01 January 1970 5,878 2 View

Is there a formula to convert a peak area' value of HPLC to concentration?

Conversion of peak area' values of HPLC to concentration!

01 January 1970 4,782 14 View

How the popular databases like SILVA and Greengenes are generated?

Hi everybody, Do you have any idea how the databases are made? In other words, what processes they take to be generated? By the way, how they collect the new sequences and their taxonomies? And...

01 January 1970 3,332 0 View

Validity of using 16S rRNA Gene for species Similarity

Hi dear researchers, While two organisms sharing ≥97% identical 16S rRNA genes may or may not belong to the same species, so why many researchers using 16S rRNA gene for their studies? For...

01 January 1970 2,803 2 View

How can I improve mcrA gene Taxonomy?

Hi all, I analysed mcrA gene reads by Qiime2. I extracted taxonomy and Sequence references from NCBI website. The result I got is unsatisfied, in my view, because many of taxa are uncultured and...

01 January 1970 1,156 0 View

Dilution of Nucleic acids' Concentration from Soil Samples Used in qPCR

Hi, Except humic acid existence in soil samples, are there other reasons to dilute DNA or cDNA concentrations of soil samples prior to performing qPCR assay? And after dilution and qPCR assay,...

01 January 1970 8,070 3 View

STAMP software for 16S rRAN dataset analsysis

I read its tutorial, but I was unable to import my data. The tutorial has made it difficult to understanding. Can you tell me how to import my data? My data is composed of multiple groups! thanks

01 January 1970 5,832 0 View

A Problem in Analysis of a Microbial Functional Gene.

I have analysed mcrA sequences in QIIME2. The mcrA database was extracted from the NCBI website, but the taxonomy barplot assigned few taxa in different ranks. In comparison to other publications,...

01 January 1970 909 0 View