Whats wrong with the Illumina sequencing?

More Sushmitha T J's questions See All

Do we save MSMEs of the Nation ?

SMEs are backbone of the country's white economy, most of them are II generation entrepreneurs and migrated from family owned business policies, and having sufficient higher educations for...

01 August 2024 5,562 2 View

How to perform EEG source analysis on each trial of data separately?

Hello Everyone I have a question about structure for connectivity analysis on sources. My goal: preprocess and cut data into trials create headmodels, using template MRI file perform source...

30 July 2024 2,743 1 View

Ti6Al4V - Phase differentiation between alpha and alpha prime martensite?

Dear Researchers, Is it feasible to distinguish between alpha and alpha prime martensite in the Ti6Al4V alloy under rapid solidification in the as-cast state using XRD, in addition to...

30 July 2024 3,849 0 View

Dear researchers. pl help how to plot jablonski energy level graph and magnetic hysteresis curve in origin?

through origin software

17 July 2024 4,990 0 View

How to make pre-post data analysis more 'sophisticated' than a paired samples t-test?

As part of my thesis I'll be conducting a single-sample pre-post intervention analysis, in which my only DV is ordinal (7-point Likert scale). In my research proposal I said that I would use...

05 June 2024 3,122 2 View

Is the "snowball metrics" mathematically well-founded?

Snowball metrics is used by scival.com to report some performance indicators. This metrics seems rather obscure from the mathematical standpoint. Unfortunately there is apparently (after a quick...

05 June 2024 7,463 0 View

What is the difference between self-renewal and proliferation?

A stem cell can divide to produce 2 identical copies of itself, which is called self-renewal. Then what is proliferation in terms of stem cells. Or is this term 'proliferation' applicable to stem...

04 June 2024 6,244 4 View

How does transient transfection of GFP plasmid works inside stem cells?

We have transfected the plasmid with lipofectamine, the plasmid will eventually move into the nucleus for transcription. Does this plasmid remain in the nucleus during cell replication? if so how...

22 May 2024 5,957 2 View

How to run an MD simulation for graphene oxide in Gromacs using CHARMM force field?

Firstly, is it appropriate to run an MD simulation for drug-graphene oxide interaction in Gromacs using CHARMM force field? If so, how can it be done? The problem that occurred was that the...

16 May 2024 5,106 0 View

How to deal with zero/negative growth rates in tree growth models?

Tree growth is an important aspect of forestry and forest ecology. Typically a growth rate is calculated as the difference between two stem diameter measurements over a given time interval: (dbh2...

15 May 2024 8,739 2 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 5,136 1 View

How to confirm the site-directed mutagenesis result without performing NGS?

I'm cloning a fragment of 3200 nts into plasmid. The cloning was successful, however, 02 amino acids were mutated. Now I want to fix these 02 aa by site-directed mutagenesis technique using...

08 August 2024 4,645 2 View

Does anyone have issues using Prepman Ultra reagent for MicroSeq ID bacterial, fungal and yeast sample preparation?

I have been attempting to extract DNA from Bacterial, Fungal and Yeast banked samples (>1e7 cells) using Prepman Ultra reagent and I seem to be struggling to obtain a sequence. Although the...

01 August 2024 2,078 0 View

Should the amount of DNA input used for ChIP-seq library preparation be matched between the control and experimental groups?

Hi all. As a beginner in ChIP-seq experiments, I hope you understand that the following questions might be somewhat basic. I am planning to perform ChIP-seq or MeDIP-seq analysis to investigate...

28 July 2024 6,938 1 View

If my gene of interest has high GC content can it be problematic in sequencing? What kind of error is expected with GC rich gene sequences??

Gene sequencing related trouble shooting

25 July 2024 4,148 2 View

Does post-translational protein modification cause devisions on observed pI verses calculated pI?

In running two-dimensional gel electrophoresis on bacterial protein, some spots that appear to match a protein sequence have a significantly more acidic isoelectric point than the calculated pI....

24 July 2024 8,075 3 View

Are there always been barcodes, apapters and primer sequences in the FASTQ files of NGS?

Hello researchers, Sorry for my stupid question. I am learning the QIIME2 workflow for analyzing some 16s amplicon NGS fastq data. I found a very nice paper with data and code public available...

20 July 2024 5,404 2 View

Promotor observation in region annotation of RNA RIP-seq?

Hello all, I extracted RNA from my samples and performed RIP-seq. After annotating the genomic regions using R, I obtained promoters, exons, introns, and UTRs. Given that my samples consist of...

18 July 2024 1,576 2 View

Analysis of MHC-I and II alleles with CNVs and unassigned loci?

I am working on a dataset of MHC-I and II alleles from a bird species sequenced with Illumina. We were not able to assign alleles to loci through MHC-typer as we were over the limit of 150 alleles...

15 July 2024 181 1 View

Why does it show two bands when I add single hairpin structures to a gel?

Hi everyone, I am working on a hybridization chain reaction (HCR) and trying to visualize it with gel electrophoresis. The visualization of the HCR works but for the single components of this...

07 July 2024 9,413 4 View

Sergio Alías-Segura

I would say there is nothing to worry about. Check https://www.biostars.org/p/9490605/

Sushmitha T J

Dear Sergio, thank you.

Abhijeet Singh

Looks like it is just one read. How many reads do you have for that sample?

Total Sequences: 32045184

Then you should just proceed with the next step in your analysis. You can't do anything anyway to change the quality of your data. But, the data is very good, probably due to the short read length. Conclusion, there is nothing to worry about.

Kuberan Ganesan

The fastqc data looks good quality-wise.