NGS - data analysis?

More Anna Stanisławczyk's questions See All

Is it Ok to decline to write a chapter for a IntechOpen to the lack of experience?

I have been asked by IntechOpen to write the chapter for a book they are going to publish, but as I don't have enough experience in the area they proposed me to write I declined their offer. Now...

24 February 2021 2,802 4 View

How to inerpret whether PCR went OK?

Dear friends! I am back to work after 3 years career break. Now performing a PCR, feeling like a newbie... Please, help to understand whether RT-PCR reaction "worked" or not. Which results should...

14 February 2021 3,129 8 View

Which fungicide are good for primary cells? Does it yeast contamination? How to get rid of them without killing the cells? How to get rid of spores?

Hello! Our lab is working with primary cells which we are isolating from the colorectal tissue. During the isolation, we are washing the tissue with pen-strep and then also add some pen-strep in...

07 February 2021 8,258 3 View

EMOJI-POLL-3 (Emoji-Association): Can you join the survey?

https://docs.google.com/forms/d/e/1FAIpQLSfaaCWZZqMIhoz5yj_5dxggvb6-cISx3GUHssYUWZWKbpx3UA/viewform Dear colleagues! We ask you to participate in a series of surveys related to the scientific...

26 January 2021 5,969 3 View

The same lC-MS for Forensic Toxicological and Chemical expertises?

Dear Colleagues! How correct and appropriate is it to carry out a forensic toxicological examination of drugs and psychotropic substances in biological objects (in blood, urine, hair) and a...

24 January 2021 4,489 2 View

GC-Headspace (HS-GC) chromatography for Forensic toxicological and Food expertises?

Dear Colleagues! How correct and appropriate is it to conduct forensic toxicological and food examination of volatile substances (ethanol, methanol, propanol, ethyl glycol, etc.) in blood and...

24 January 2021 5,645 2 View

How to choose mouse cell line to work on?

Hey, I am looking to start working on mouse cell line for some genomics experiments. I have the following requirements: 1) Normal chromosomes composition. 2) Possible to transfect. 3) Possible to...

03 January 2021 4,387 2 View

How to describe the method described below?

I do research on the relationships between universities and local governments by asking the research question (how) can universities contribute to the design (and implementation) of public...

29 December 2020 4,522 12 View

How can I change the media for THP-1 cells without dislodging them from the surface of my well plate?

I am working with THP-1 cells at the moment and am having trouble with maintaining a high confluence once I seed them on a 24-well plate. I usually try to seed around 100,000 cells per well and...

29 December 2020 1,567 3 View

What glass vials do you use for small volumes (400ul-2000ul) that fit in the centrifuge?

I am planning some NMR experiments that require glass vials (due to chloroform). I am looking to find glass vials that would take 400-2000ul volumes, fit in the centrifuge and allow me to separate...

01 December 2020 3,259 2 View

How to compare two groups with only two measurements?

Hiiiii everyone! I have an enquiry on statistical analysis. I was looking for many forum and it's still cannot solve my problem. I want to compare means of two groups of data but only with two...

03 March 2021 8,796 3 View

How to analyze a particular region of my simulation box in GROMACS?

Hi, I am using GROMACS 5.1.4 to simulate water in contact with a surface. I am only interested to calculate some properties of water near the surface. Let's say at a distance of x nm from the...

03 March 2021 9,989 2 View

Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence?

I am on the lookout for the Enhanced Yellow Fluorescent Protein (Aequorea victoria) DNA sequence. Does anyone know where I can find it? Thank you in advance

03 March 2021 3,568 1 View

What kind of fluid could I use for a pitfall trap that also does not invalidate molecular testing?

Hi, I want to start testing pitfall trap to obtain ants samples, but I need to conduct molecular analysis on those insects. So, what kind of fluid can I use? Ethanol expires too early and I need...

03 March 2021 5,978 5 View

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10?

What's the best way to measure growth rates in House sparrow chicks from day 2 to day 10? Since, the growth curve from day 2 to 10 won't be like the "Logistic curve" it might not follow logistic...

03 March 2021 1,401 3 View

Do we need to write protocol for a second study of a systematic review that has been registered and published?

I have conducted and published a systematic review and meta-analysis research with the topic related to public health and health pomotion (protocol was registed in PROSPERO). Now we want to...

03 March 2021 8,920 3 View

How to increase a model accuracy ?

dear community, my model is based feature extraction from non stationary signals using discrete Wavelet Transform and then using statistical features then machine learning classifiers in order to...

03 March 2021 6,994 5 View

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature)?

1. What is the impact of having different scales in a survey? and how can we solve this problem before and after data collection (Literature-based reflection)? Thank you for your time and for...

03 March 2021 2,870 3 View

What degree of missing data in a particular case/participant results in Expectation-Maximisation no longer working?

I'm dealing with a mediation model and am using the PROCESS module in SPSS. Due to SPSS and PROCESS being limited in the imputation methods - being unable to handle multiple imputation - the other...

02 March 2021 4,362 1 View

How to get onecolumn document from standard IEEE ACCESS LateX template?

I have prepared a manuscript in IEEE Latex template, but for some purpose, I need to prepare a word file as well (detailed format is not required). Compared to two column .tex file, one column...

02 March 2021 1,830 3 View

Ankur Das

use plink version 1.9 or above and run the following command:

plink --bfile my_file_prefix --recode vcf --out my_output_file_prefix

Good luck...

Erik Diaz

You need to first understand some concepts here. VCF files are a catalog of genomic positions that contain polymorphisms within the reads that mapped to a reference genome coordinate. VCF files are generated by analyzing the CIGAR info within the SAM/BAM alignment files. There are specialized software to identify such polymorphisms such as GATK, freebayes, SAMtools. So the question of convert a BAM to a VCF is actually wrong. You should first read some review papers on the topic, and then run the actual analysis.

Aqib Sarfraz

Dear Anna Stanisławczyk you can use BEDOPS v2.4.40 package vcf2bed script. please go through the below mention link.

https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/vcf2bed.html

Good luck