Tag: fastQC

identify and remove adapter sequence

identify and remove adapter sequence 2 Hi all, I am trying to identify the adapter sequences of my ATAC-sequencing data. The way I tried to achieve this was to send the fastq file to FastQC. Hoping the sequence would be picked and showed in the report. In the report, there…

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FastQC analysis

FastQC analysis 0 Hii, Could anyone please tell me if I can carry out the FastQC analysis using data available online and not in my system? The sequence data that I want to check is huge so was wondering if there was any way to access them online through FastQC?…

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ChaoXianSen/TrimGalore – Giters

Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. Installation Trim Galore is a a Perl wrapper around two tools: Cutadapt and FastQC. To use, ensure that these two pieces of software are available…

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python – Missing input files after defining them in function

I am trying to do QC on RNAseq data that is tarballed. I am using Snakemake as a workflow manager and am aware that Snakemake does not like one-to-many rules. I defining a checkpoint would fix the problem but when I run the script I get this this error message…

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Index of /readarchive/Miseq/2014_05_21_run_miseq/Adapter_trimmed_nextera_samples/QC_after_trimming/Geo33_S19.R1.trimmed.paired_fastqc/Images

Name Last modified Size Description Parent Directory   –   duplication_levels.png 24-May-2014 17:58 17K   kmer_profiles.png 24-May-2014 17:58 433K   per_base_gc_content.png 24-May-2014 17:58 48K   per_base_n_content.png 24-May-2014 17:58 26K   per_base_quality.png 24-May-2014 17:58 32K   per_base_sequence_content.png 24-May-2014 17:58 96K   per_sequence_gc_content.png 24-May-2014 17:58 25K   per_sequence_quality.png 24-May-2014 17:58 19K  …

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Average Read length

Average Read length 3 Hello Everyone! Is there a standard tool commonly used to calculate the average read length of fastq files? If yes please mention it here because I want to know the size of average reads of my fastq files so that I can decide the cutoff for…

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Different FastQC results after name-sorting BAM file, sequence duplication increases

Different FastQC results after name-sorting BAM file, sequence duplication increases 1 Okay, so what I did might was stupid, but I was determined to examine on my own a lot of things, and experiment a bit with tools. At one point I decided to do this: I had BAM file…

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Total sequences – FASTQC report

Total sequences – FASTQC report 1 Hello! Can someone please dummy-explain to me what exactly are total sequences? I am practicing some bioinformatic problems and in my FASTQC report I get this: Total Sequences 85988702, Sequence length 76. Does that mean that I have one target region of interest with…

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Find right adapter sequence for trimming

Find right adapter sequence for trimming 0 Hello everyone I am newly start to working RNAseq analysis. I am trying to clean single end reads data according to fastqc result. It was resulted like in example as SRR309133 I was tried Illumina Adapter Sequences find it there.But after trimming result…

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16s rRNA Sequencing Meta-analysis Reconstruction Tool (using mothur).

16SMaRT is a bioinformatics analysis pipeline for 16s rRNA gene sequencing data. 16SMaRT is a “one-click” solution towards performing microbial community analysis of amplicon sequencing data. 16SMaRT aims to be your go-to solution for your next microbiome/metagenomics project. The primary objective of 16SMaRT analysis is to determine what genes are…

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get rRNA FASTA file for a particular bacteria

get rRNA FASTA file for a particular bacteria 0 Hey all, I was trying to find a way to get all rRNA (5S, 16S and 23S) FASTA sequences for a particular bacteria (B. thetaiotaomicron VPI-5482, which is the type strain). I wanted this file so that I could use something…

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Trimming DNAStringSet

Trimming DNAStringSet 1 Hello, I am currently dealing with the problem of reading in a Fastq-File with “readDNAStringset”, trimming the Sequences and then writing them in to a new fastq-file. The reading of the fastq-file with “readDNAStringSet” is working just fine. I am then trying to trim a fixed length…

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Scripts for BGC analysis in large MAGs and results of their application to soil metagenomes within Chernevaya Taiga RSF-funded project

This repository include scripts for analysis of biosynthetic gene clusters (BGCs) in large metagenome assemblies. All scripts were created within the Chernevaya Taiga project funded by the Russian Science Foundation (grant 19-16-00049). The repository also contains results of the scripts application to four hybrid (illumina + ONT) assemblies of various…

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Single-cell DNA and RNA sequencing reveals the dynamics of intra-tumor heterogeneity in a colorectal cancer model | BMC Biology

Organoid culture of small intestinal cells and lentiviral transduction C57BL/6J mice and BALB/cAnu/nu immune-deficient nude mice were purchased from CLEA Japan (Tokyo, Japan). The small intestine was harvested from wild-type male C57BL/6J mice at 3–5 weeks of age (Additional file 1: Figure S9A). Crypts were purified and dissociated into single cells,…

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How can I get PHRED score?

How can I get PHRED score? 1 Hi, all. I am trying to get the assembly stat(Table S1.) according to the following paper about de novo assembly. [www.ncbi.nlm.nih.gov/pmc/articles/PMC7266049/%5D%5B1] In the table, there is an item “Mean read PHRED score after filtering and trimming”. How can I get this? Is there…

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The sardine run in southeastern Africa is a mass migration into an ecological trap

INTRODUCTION Large-scale annual migrations occur in an extraordinary range of animals, from insects to the great whales. While the driving mechanisms of these migrations are varied and sometimes poorly understood, they often represent a way of optimizing conditions for breeding and adult fitness when these are in conflict. Often, populations…

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I downloaded fastq files from a repository and tried to run fastqc, how can the average sequence length be only 8 bp?

I downloaded fastq files from a repository and tried to run fastqc, how can the average sequence length be only 8 bp? 1 I downloaded sequencing files from 2 patients from here: www.ebi.ac.uk/ena/browser/view/PRJNA588461?show=reads there is one fastq file for the forward (1) and reverse (2) reads. I wanted to look…

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Should I expect high duplicate read frequency in my scRNA fastq’s?

Should I expect high duplicate read frequency in my scRNA fastq’s? 0 Hi there, I’m new to scRNA-seq data and I am looking at a multiqc report for some of my samples. The screenshot below shows the sequence counts for my fastq’s. My question is, should I expect such a…

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Fastqc user manual – vodosp.ru

FASTQ format – Wikipedia 06 September 2021 – by TC Collin · 2020 · Cited by 3 — Be accompanied by a step-by-step user-friendly manual, If the user performs FastQC prior to the removal of adapters (step 3), the length Both programs can be used on Linux/MacOS X machines and quite…

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Weird 8bp peak in (clean) small RNA data

Weird 8bp peak in (clean) small RNA data 0 Hi everyone, I’ve received some small RNA sequencing data from a collaborator and after removing adapter and trimming (with TrimGalore) i have a small peaks at ~20 and 30 bp, as I was expecting, plus a huge peak at 8bp that…

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FASTQC not showing adapters—cutadapt sanity check—

Hello a newbie here, I am reanalyzing an article (GSE83931) for training purpose. I have two concerns/question. 1- I performed FASTQC on the sequences followed by multiqc. When I look at the reports individually it doesn’t show any adapter sequence. (please see pic1). (Authors reported the they used Trimmomatic to…

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Gene mutation analysis in papillary thyroid carcinoma

Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…

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How to view fastqc output file in html format which is on remote server

How to view fastqc output file in html format which is on remote server 1 I currently have few html fastqc output files on a remote server that I ssh to. I want to visualize it in my browser. How can I do this? remote linux ssh • 22 views…

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An epigenetic basis of inbreeding depression in maize

INTRODUCTION Charles R. Darwin documented inbreeding depression as growth disadvantages from self-fertilization compared to outcrossing in many plants (1). Prevailing hypotheses suggest that inbreeding depression results from the exposure of deleterious recessive alleles and/or loss of overdominant alleles due to increased homozygosity (2, 3) or reduced recombination frequency in some…

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Global phylogenomic analyses of Mycobacterium abscessus provide context for non cystic fibrosis infections and the evolution of antibiotic resistance

1. Lee, M.-R. et al. Mycobacterium abscessus complex infections in humans. Emerg. Infect. Dis. 21, 1638–1646 (2015). CAS  PubMed  PubMed Central  Google Scholar  2. Prince, D. S. et al. Infection with Mycobacterium avium complex in patients without predisposing conditions. N. Engl. J. Med. 321, 863–868 (1989). CAS  PubMed  Article  Google…

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Any program to check resources used by Bioinfo Tools

Any program to check resources used by Bioinfo Tools 0 Hello Everyone, I have a bash Script of FastQC and Trimmomatic. I want to know how much resources each of these tool uses. So is there any way or any bash command or tool which helps with this situation. If…

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removing adaptor

removing adaptor 1 I have two RNAseq datasets, from two different sequencing core facilities – the fastq files they provide already are demultiplexed and trimmed for adaptor. This is the Adaptor content following fastqc-> multiqc . According to the multiqc all files passed the qc for adapter content. So I…

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Pybedtools error sans

Pybedtools error sans 20-08-2021 pysam – Error when I install samtools for python on windows – i trying install pysam, pybedtools modules on python got error: ($i=1; $i[email protected] temp]$ conda install pysam bedtools hisat2 [ snip. However,…

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Trimming Nextera adapter from scRNA paired reads with different length

Trimming Nextera adapter from scRNA paired reads with different length 0 Hi everyone, I have two FASTQ files (R1 and R2) which R1 is 50bp (cDNA) and R2 is 17bp (BC+UMI). I would like to trim the Nextra adapters with Trim Galore and to keep only reads that are >35bp…

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Is it normal for RCorrector to remove millions of reads?

Is it normal for RCorrector to remove millions of reads? 0 I’m trying to build De Novo transcriptomes for unsequenced plants to do sequence analysis. I’m trying to choose a tool for my first pass of quality filtering after running FastQC on my raw reads. I’ve tried AfterQC and RCorrector….

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How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ?

How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ? 0 A colleague of mine have got the following distribution of GC-content for RNAseq. How to interpret bimodal distribution of GC-content for RNAseq ? Does it mean some contamination ? Is there any method to…

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