Tag: mnp

IJMS | Free Full-Text | CRISPR/Cas9 Directed Reprogramming of iPSC for Accelerated Motor Neuron Differentiation Leads to Dysregulation of Neuronal Fate Patterning and Function

1. Introduction As the world population ages, neurodegenerative diseases are increasing. The outcome of these diagnoses varies but can lead to fatality 50% of the time within 15–20 months [1]. Treatments for neurodegeneration, in particular motor neuron (MN) diseases, are restricted due to the limitations of motor neuron repair and…

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The Therapeutic Effects of MUC1-C shRNA@Fe3O4 Magnetic Nanoparticles i

Introduction Breast cancer (BC) is a malignant tumor originating from the epithelial tissue of the breast and is the most common malignancy in women.1 It is estimated that by 2040, there will be 3,000,000 new cases of BC and 100,000 deaths worldwide. Triple-negative breast cancer (TNBC), which accounts for 15–20%…

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Oligonucleotides | Thermo Fisher Scientific

Use this tool to design a custom DNA oligonucleotide, with any of a variety of 3′ and 5′ modifications, at scales ranging from 25 nmole to 10 µmole. Select desired purification method (normal or reversed-phase chromatography, HPLC, or PAGE). Use this tool to design a custom DNA oligonucleotide, with any…

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error related to SnpSift

error related to SnpSift 1 hello everyone, I am trying to use annotate function of snpsift. I have downloaded the software using conda. when i write the command SnpSift this is the output: SnpSift version 4.3t (build 2017-11-24 10:18), by Pablo Cingolani Usage: java -jar SnpSift.jar [command] params… Command is…

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GenomicsDBImport from Mutect2 output

I am trying to follow GATK 4.2.0 best-practice guidelines for Mutect2 PoN creation. I called variants in my samples as recommended with: gatk Mutect2 \ -R ${REF} \ -L ${EXOME_INPUT_INTERVALS} \ -I ${BAM} \ –sequence-dictionary ${DICT} \ –max-mnp-distance 0 \ -O ${SAMPLE_NAME}.mutect2.vcf but I see that the tool is unable…

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At every stage from farm to table, more microplastics enter your food

A new study has found that, globally, micro- and nanoplastics and plastic additives are widespread across our food supply. While we have an understanding of how they get there, we don’t know a lot about their effects on human health, food safety and security. The average person discards about 77…

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combine/merge closet variants into one from mutect2

Using GATK Mutect2, we collected several variants in EGFR region. However, one variants NM_005228.5(EGFR):c.2239_2248delinsC (p.Leu747_Ala750delinsPro) were called as two separated ones. The two variants can not combined even we set the -max-mnp-distance to 20. 7 55242465 . GGAATTAAGA G . .AS_SB_TABLE=5567,5732|44,36;DP=11794;ECNT=2;MBQ=20,20;MFRL=188,168;MMQ=60,60;MPOS=39;NALOD=3.85;NLOD=1755.82;POPAF=4.52;TLOD=256.20 GT:AD:AF:DP:F1R2:F2R1:PGT:PID:PS:SB0|1:2957,80:0.027:3037:1304,28:1306,51:0|1:55242465_GGAATTAAGA_G:55242465:1402,1555,44,36 0|0:8342,0:1.710e-04:8342:3598,0:4195,0:0|1:55242465_GGAATTAAGA_G:55242465:4165,4177,0,0 7 55242478 . G C . .AS_SB_TABLE=5360,5529|44,36;DP=11030;ECNT=2;MBQ=20,20;MFRL=189,168;MMQ=60,60;MPOS=43;NALOD=3.93;NLOD=1686.18;POPAF=4.52;TLOD=256.12…

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“Lollipop” particle counting immunoassay based on antigen-powered CRISPR-Cas12a dual signal amplification for the sensitive detection of deoxynivalenol in the environment and food samples

Deoxynivalenol (DON) is one of the subgroup B mycotoxins, mainly produced by Fusarium species, and reported to be the predominant contaminant in the environment and food [17], [26]. The toxic effects of DON include immune modulation, disruption of intestinal barrier function, and cytotoxicity leading to cell death [13], [8]. Due…

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RDS file in Rstudio

RDS file in Rstudio 0 Hello, I have downloaded the RDS file here, the “MNP-VERSE”. I am trying to extract all the cells and their value for a specific tissue in a specific gene (e.g. breast tissue and MSR1 gene). So far I get this: library(tidyverse) filename <- file.choose() msr1…

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Extract differen variants of a vcf file comparing to vcf files

I have a treatment vcf file and three control vcf files. This has been generated from somatic variants on RNAseq data. I want to extract variants that are in treatment sample but not in control groups. To do so, I first normalized them using bcftools norm -m -any command, then…

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Issue with VCF format while using Pharmcat

Hello everybody, I am using pharmcat tool’s prerprocessor feature to preprocessmy vcf file using the command > python3 pharmcat_vcf_preprocessor.py -vcf sample.vcf But I think there is some issue with my vcf file as this command outputs an error > Reading samples from sample.vcf … Saving output to . > >…

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Platypus

Platypus 0 Hi, I’m super new to WGS and bioinformatics, but I’m a classic software data scientist, so I know enough to be annoying. I’m using Platypus too call variants on 100X WGS via Nebula Genomics. I found an odd series of calls and am not sure if this is…

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