Is there any tool or web server available for prediction of mutational hotspot in a RNA?

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What shoud i do if multiQC stats from featurecounts show that only 3% of my aligned reads is assigned even 70% of my reads are aligned in STAR?

During my RNAseq data analysis, I encountered a problem where the statistics from MultiQC from the STAR method showed that 70% of my trimmed reads were aligned, but when I ran using the same BAM...

04 January 2024 6,157 1 View

Query regarding RNA seq data analysis?

I was performing a RNAseq data analysis. I did my alignment using RNA-STAR and then I perform featurecounts. I used latest assembly of human genome i.e. HG38.p14. But after feturecounts step i...

26 September 2023 3,278 3 View

Limit of biological replicate for RNA-seq data analysis?

I'm performing RNA-seq data analysis. I want to do healthy vs disease_stage_1, Healthy vs disease_stage_2, and Healthy vs disease_stage_3. In the case of healthy, disease_stage_1, disease_stage_2,...

02 May 2023 9,816 3 View

How to assemble human genome from illumina paired end sequencing?

I have 3 Illumina paired-end sequencing data of humans. I want to assemble these 3 genomes. My final goal is to retrieve some gene sequences from these 3 genomes. So, 1) Please suggest to me any...

24 January 2023 7,493 4 View

Can someone please explain the interpretation of Nucleotide Diversity (Pi) value for a viral Alignment file?

I used DnaSP software to perform a nucleotide diversity analysis on a viral alignment file. After observing the data I saw that some positions have high values (0.79) and some positions have lower...

25 November 2022 3,522 1 View

Can anybody suggest me a pipeline to assemble chromosome specific human genome?

I have human WGS raw reads and paired-end data. Illumina Hi-Seq 2000 was used for sequencing. I want to assemble this genome either de-novo or reference-based. I want to assemble it...

12 June 2022 4,218 3 View

How can I run a sequence identity analysis or clustering of 2 million sequence?

Hi, I have over 2 million nucleotide sequence and each sequence is average 30kb in size. I want to run A sequence identity and clustering analysis on that..I tried CD-HIT suite but it falling...

01 November 2021 7,799 4 View

Is there any way to download all whole genome at once from GISAID database instade of 10k per time???

I'm trying to download whole genome of alpha strain COVID-19 from GISAID database.in alpha strain 2 million sequence are there.and in that database, it is showing that I can download max 10k per...

27 October 2021 7,976 1 View

Tools to perform whole genome clustering by 100% sequence identity?

I have whole genome data sets of SARS-Cov2 of different countries. Now I want to exclude genome sequences which represents 100% sequence similarity. I want to do it by clustering analysis.. 1)...

11 May 2021 9,763 3 View

Is there any tools available to do a mutation analysis in phylogeny?

I had 1 set of 11 protein coding nucleotide sequences of 11 primates Species. and i draw a phylogenetic tree . I want to know the no of mutation has occur in each branches or want to know the...

10 March 2021 7,685 3 View

How to learn more about SPSS and its Application?

I would like to learn more about SPSS and Its application especially in regards to data analysis. Please suggest me how I can learn more about it. Thank you so much.

11 August 2024 9,101 4 View

Is there a problem with my RNA pellet?

Hello, I am currently having problems with RNA extraction. I am using mouse liver (C57BL6J), and I have extracted RNA from mouse liver before. Before this experiment, my final RNA pellets were...

11 August 2024 7,082 3 View

Can I base on reverse DNA sequences to perform alignment, convert to amino acids and GenBank submission?

I have reverse sequences (AB1 format), can I base on reverse DNA sequences to perform nucleotide alignment, convert nucleotides to amino acids and deposit the sequence in GenBank database?

11 August 2024 5,138 1 View

Baseline drift in HPLC? What causes this?

Hello, Why do i see this baseline drift when i compare my blank (black) to the sample (blue)? Any suggestions as to why this happened? Thank you!

11 August 2024 3,770 4 View

Text-Communication from the M1 Hand Area using BCI—and then there is Elon Musk?

Willett, Shenoy et al. (2021) have developed a brain computer interface (BCI) that used neural signal collected from the hand area of the motor cortex (area M1) of a paralyzed patient. The...

10 August 2024 7,180 0 View

Has anyone applied Python in the field of textile engineering for data analysis, automation, or smart textiles?

I'm currently exploring the application of Python in textile engineering, specifically in areas like data analysis, process automation, and the development of smart textiles. I'm interested in...

10 August 2024 7,429 2 View

Strugglling with m6A dot blot any suugesstion ?

I have been doing the m6A dot blot for a while with no improvement, I am extracting the RNA, and I can see the dots although the three biological replicas give a different reading on the memberan...

10 August 2024 8,539 5 View

How can I use the cif data obtained from rietveld refinement extracted via gsas2, for microstructural analysis using ETEX software?

09 August 2024 7,718 0 View

RNA Extraction Using Hot Borate Method No Longer Working?

I've been performing RNA extraction on cotton petiole tissue for a few months now using the method described in the following paper, a derivative of the typical hot borate method...

08 August 2024 9,882 2 View

Does Anyone have expertise in in vitro transcription and RNA pull down assay?

I am currently working on LncRNA; to know the lncRNA-protein interactions I want to do RNA pull down assay, so I need to design primers with T7 promoter. I need assistance in this regard.

07 August 2024 6,622 1 View