Questions tagged [ngs]
use for general applications of high-throughput nucleotide sequencing methods that use short-read technology (e.g. Illumina, IonTorrent). For long-read sequencing, use 'long-read', or a more specific tag if applicable (e.g. nanopore, pacbio).
282
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Are there packages that can infer a sample's aneuploid cell proportion using sequencing data?
I have low-coverage WGS data from embryonic tissue (4-6 cells taken from early embryonic tissue). The exact number of cells is unknown and there's no strong prior on the aneuploid fraction, but I don'...
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"BLASTx for miRNA Annotation: Mature vs. Primary miRNAs as Query Sequences"
I am doing miRNA annotation of a plant genome. I have two files - one containing all the predicted mature miRNAs and another containing all the predicted primary miRNAs. I want to find out which are ...
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Recent Bioinformatics Graduate Seeking Resources for NGS and Drug Discovery [closed]
I recently graduated with a bachelor's degree in bioinformatics. Unfortunately, the bioinformatics program at my university was limited, and I'm feeling the need to expand my knowledge in specific ...
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3
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3
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Best practices for handling single-end and paired-end data in a Snakemake pipeline
I am fairly new to Snakemake and am building an NGS data processing pipeline to align ChIP-seq data and call peaks on it, plus some other analyses. The data can be single-end or paired-end, depending ...
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Where to obtain fastq_illumina_filter
I'm setting up a snakemake pipeline for my lab, and I'd like to install fastq_illumina_filter. All links I can find point to this address for info on it, but the website seems to be down.
Is there ...
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2
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70
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Issues with adapter trimming (Trim Galore)
I am new to coding and especially new to bioinformatics so I am sorry if this is a dumb question. Nevertheless, I am attempting to run Trim Galore! to trim my paired RNAseq data, there are no error ...
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76
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RNA-seq QC and alignment error in script
I am analyzing bulk RNA-seq data for Paired-End. I have separate scripts for fastqc, STAR & qualimap but want to run them in a single script which looks like this
USAGE: sh rna-qc.sh <path/to/...
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2
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1
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GBS- 'Failure' in, Per base sequence content, Sequence Duplication Levels, and Adapter Content
I have a GBS sequence on the Illumina platform that in the FASTQC quality report has “Failure” in : Per tile sequence quality, Per base sequence content, Sequence Duplication Levels and Adapter ...
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How to extract the mutations specific to cancer after variant annotation in NGS analysis
I am working on B cell lymphoma of dogs to identify the specific type of mutations related to this disease. I am performing NGS whole genome sequencing analysis. I have performed the variant ...
2
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1
answer
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How much data to expect from metabarcoding?
I am about to conduct my first metabarcoding study. We will be using the ITS amplicon to look at fungal community composition in soil samples.
I need to write a data management plan before I actually ...
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1
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1
answer
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SNP Signatures with Limited WGS Data:
On 80 WGS samples, I'm dissecting SNP signatures linked to milk production in a scarcely studied animal. Post-variant calling and QC association analysis have been tricky. I'm here to tap into our ...
- 386
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Can index hopping lead to more reads in samples?
We run multiple samples for sequencing on an Illumina NovaSeq machine. After converting the files to fastq format using bcl2fastq, we can see that we have some ...
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49
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4
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1
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split fastq file containing a sequence block at different locations
I have some fastq files (obtained from nanopore sequencing) that contain reads that can be of either of these 5 forms:
a known CDS with 3'UTR:
...
2
votes
1
answer
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Approaches for filtering bacterial/fungal contaminant sequences from RADseq results
I'm working with RADseq data (288 compressed FASTQ files, *.fq.gz) from 3 plates of plant tissue. I've done demultiplexing and preliminary QC (using the Stacks <...
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