Questions tagged [sequencing]
DNA sequencing is the process of determining the precise order of nucleotides within a DNA molecule.
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CRISPR/Cas9 screen analysis with Mageck: paired-end sequencing
I want to analyse data from a CRISPR/Cas9 screen (control vs. treatment) and I'm using Mageck (https://sourceforge.net/projects/mageck/). The problem is that I'm working with paired-end sequencing ...
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76 views
Sequencing center returns data in several files
We send some samples to sequence and we got several (fastq.gz) files for each sample. The files are distributed at two or three folders with different dates (more than a week apart). The dates of the ...
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62 views
Coverage required
I was came across a problem during an exercise in a book and I don't really know how to solve it. I feel like something's missing.
"coverage, c = $NL/G$ (N=number of reads, L=read length, G=genome ...
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How to best detect the “peaks” in RNA-seq data that are not assigned to any gene?
I encountered that many reads from single-cell RNA seq data were lost in the analysis because not assigned to any gene (genome: galgal6). I am trying to find an approach than could give me all the "...
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High percentage of poly A sequences in 10X chromium R2 read
I'm currently analyzing two samples of eosinophil cells isolated from mouse lung and the samples are of very different quality.
According to the Cell Ranger summary 56% of the reads can be mapped to ...
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What is the name of this type of figure?
This figure comes from this wiki page.
I googled "gene location figure" and "gene location plot", none gets similar results. I also tried search by image, none of the results is close.
so, what is ...
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69 views
How to reproduce this specific sequence logo from 10 000 human mRNAs?
this is A sequence logo showing the most conserved bases around the initiation codon from 10000 human mRNAs.
I would like to reproduce this sequence logo. How can I get the sequences? which database ...
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31 views
Is there a convention or standard of the highest bits in a sequence logo? [duplicate]
In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).
wiki says
The total ...
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40 views
what does a sequence look like before alignment?
I am confused with Sequence alignment, which is
a way of arranging the sequences of DNA, RNA, or protein to
identify regions of similarity that may be a consequence of
functional, structural, ...
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113 views
How to compute the Shannon entropy for a strand of DNA?
I'm confused by the computation of sequence logo. Wikipedia gives a process about this without a concrete example.
Let's just consider DNA, so there are 4 bases (nucleic acids).
The following data ...
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1answer
80 views
Why do ten rows (Figure_1) correspond to 2 bits (Figure_2) in a sequence logo?
Following this question, I'm confused with the computation of sequence logo
Following data comes from the book "Machine Learning - A Probabilistic Perspective (Figure_1)"
here is the corresponding ...
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136 views
What is “aligned sequences” and “consensus sequence” in the context of sequence logo? How to compute these?
In bioinformatics, a sequence logo is a graphical representation of the sequence conservation of nucleotides (in a strand of DNA/RNA) or amino acids (in protein sequences).
so, What is "aligned ...
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132 views
Paired end sequencing with R1 and R2 of different length. Possible?
There are commercial sequencing kits/sequencers that allow for paired end sequencing in which the two reads obtained for each fragment are of different length?
For example 150bp for R1 and 50bp for ...
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1answer
59 views
Produce a single sequential FASTA sequence out of BAM
I'm having problems properly looking for a solution because I'm a layman in Bioinformatics not familiar with the terminology. I'm hoping you can nudge me in the right direction, please! Thank you very ...
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1answer
58 views
Mixcr batch processing
I have a folder with 150 pairs of fastq files from an illumina sequence run. I need to precess them with mixcr, how can I do this in a batch with a single command?
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98 views
Crossover question from Coding Theory
I have a model that, for a given bit of code will produce a binary string. An example is given 01010101, it might produce {1,11}, and given 01010000, it may produce {2, 11}.
I have a lot of these ...
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39 views
Genotyping technologies do not maintain phase?
Why exactly does genotyping not maintain phase? I guess I'm more confused on what's the difference between sequencing and genotyping, and as a result how phase is maintained in one, but not the other. ...
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71 views
Short reads vs long reads with regards to break points
My professor in class said the following statements.
Short reads can map break points
Long reads can disambiguate repeat related issues
I'm very new to genomics, so I don't quite understand the ...
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3answers
105 views
Tools for quality trimming at 5 prime?
I'm looking for a tool that is capable to do quality trimming at 5' end and it is configurable. For example, I can choose the quality trheshold, the read length, etc. Any recommendations?
I'm ...
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1answer
407 views
Significance and timing of “mux scans”
I'm using MinIONQC to do quality control on some ONT data. The software plots several read characteristics over time (hours passed during the sequencing process). These plots contain several vertical ...
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1answer
60 views
Are there any Genome in a Bottle-like resources for non-humans (especially for invertebrates)?
Genome in a Bottle is an excellent resource that provides many types of DNA and RNA sequencing reads for a single individual/cell line to test genome assembly and analysis tools. For example there are ...
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2answers
104 views
Separation of mixed plasmid DNA sequences post whole-plasmid sequencing
Imagine a DNA sample containing a mixture of different intact plasmids. These samples are sequenced using either MiSeq or HiSeq sequencing. Would it possible to assemble these plasmids post-sequencing ...
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94 views
Where to Download Cancer Raw Reads (fastq)?
Does anyone know where I can download cancer raw reads (fastq files), tumor and Germline for non-humans?
I wanted to make a study with human data but I don't have the control access to download raw ...
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139 views
How to cluster the human genes by pathways/system-biology/metabolic properties?
I would like to make a chord plot from my data. I have a list of genes that according to my experiments are divided into 64 clusters of enrichment pattern.
I would combine my 64 clusters with a ...
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1answer
357 views
Why do I get so many insertions from Minimap2 on my Nanopore WGS?
I'm a starting my analysis on nanopore whole genome sequencing. I start my analysis from this popular Github.
The sample I downloaded was WGS for NA12878, so I would assume it's alignment to GRCh38 ...
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2answers
472 views
Hardware Requirements (specs) for Bioinformatics-dedicated desktop [closed]
I know this is a somewhat general or vague question, but I’m interested in your opinions. I must build a desktop for general bioinformatics activities with human genomes. I will work with Python and R ...
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56 views
How to score how densely bases are distributed along a given oligo?
Suppose I have a short chain string of oligos, and I want to rate them from 0 to 1 based on how clustered the "A"s are in respect to the chain. For example:
...
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1answer
505 views
Why does this human bam file only have one copy of each chromosome?
As we know that in human DNA sequence, one copy of chromosome comes from mother's DNA and another copy comes from father's DNA so as to form two copies of each chromosome in human DNA. So, if we ...
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6answers
321 views
Identifying Indels from Chromatograms
I have around 100 chromatograms (.ab1 files) from Sanger sequencing a genome at loci believed to have an indel.
I'm new to interpreting this kind of data in ...
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30 views
Sequencing Deciduous Plants
Firstly, I'm personally not in the field of Bioinformatics, so apologies if this is a dumb question.
Does anyone know of any research that has been carried out on the sequencing of deciduous plant ...
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3answers
164 views
Is there a read mapper that allows input in SAM format instead of FASTA/FASTQ?
When we get raw sequenced reads in FASTQ format, we usually need to do some pre-processing (QC, demultiplexing, etc.) prior to sequence alignment. The only way to register the results of this ...
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1answer
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E.coli Sequencing & Analysis
I have been given the task of assembling a 'new' Ecoli genome and analysing the genes present etc.
The Ecoli is a new strain, and has been taken and run on a Nextseq 500 in high-output mode with ...
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208 views
What i5 index should I use on the Illumina sample sheet for an unindexed p5 primer?
I have an upcoming run on a HiSeq X and most of the libraries in the pool have both i5 and i7 indices. However, some of the libraries were made with the IS4 p5 oligo and it is unindexed.
The IS4 ...
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561 views
Why are there more barcodes than GEMs in 10X chromium data?
Question: Why are there more barcodes than GEMs in 10X chromium data?
Introduction
I have several 10X genomics chromium libraries made with the de novo assembly/genome protocol. The 10X chromium ...
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3answers
2k views
What is the index fastq file (sample_I*.fastq.gz) generated when demultiplexing Illumina paired-end runs?
What is the index fastq file that comes with some Illumina sequencing datasets? (The samplename_I*.fastq.gz file.)
For example, I recently received some 10X ...
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1answer
84 views
Extracting sequences from FASTA beginning with common 5' end
I am trying to figure out the best way to extract sequences from a FASTA file which begin with a common 5' region of 43 nucleotides. Preferably, I would like to to allow for "fuzziness" in this region ...
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dog coordinates (canFam3) to human coordinates (hg19)
I've converted dog coordinates to human using UCSC LiftOver. These are 200bp intergenic regions that are differentially methylated from normal dogs to cancer dogs. I've converted these to human ...
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2answers
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Deciding which samples go in which batch
I have 370 samples to sequence, we probably will end up using only 96 samples per run (due to the barcode with the primers we'll use). This means running 4 batches. To minimize the batch effect I need ...
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1answer
214 views
How many reads do I need to cover the entire genome?
Suppose my genome is 3 million bases and that my reads are 100 nucleotide long. I need to know how many reads I need to cover the entire genome.
I start from using the equation $C = \frac{N \cdot L}{...
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Find the date that sequencing was performed
I've got a bunch of RNAseq datasets from ENCODE and I'm looking to identify variables contributing to variance among my samples.
For example, is there any easy way to find out the precise date which ...
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1answer
86 views
Tumor sample and heterozygous SNVs: what is the genotype of the normal cells?
In the following picture, you can see that in normal cells (yellow) we have two copies of each gene, while in tumor cells (violet), we just have one copy due to a clonal mono-allelic deletion. I do ...
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2answers
86 views
Use of heterozygous SNPs in cancer research: why?
When reading about allelic fraction (AF) and SNPs in cancer research, they always mention the fact that they're using heterozygous SNPs (informative SNPs). Why is this? Why can't we use homozygous ...
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1answer
73 views
Difference between copy number neutral reads and active reads
In this paper, the authors talk about copy number neutral reads (as reads that equally represent parental chromosomes) and active reads (as reads from only one parent chromosome):
We reasoned that ...
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1answer
116 views
How to create a nexus file for BEAST?
I am learning to use BEAUTI and BEAST software. I followed their tutorial and was able to run example data without any problem. Now, I want to do phylodynamic analysis on my data. I have downloaded 70 ...
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1answer
51 views
Help Adjusting Bedtools Output in R
I have been asked to write a script in R to edit, using data.frame, this .fa file that is the result from extracting gene sequences from a repeat masker coordinate file on the genome I am working with....
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Which software is recommended for sequencing primers selection?
I have a list of primers for sequencing fungal ITS1/2 regions. I also have access to different fungal databases. I would like to perform in silico PCR analysis for comparing different primer pairs and ...
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1answer
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Is it OK to use Blast+ to query NCBI's 16s rRNA database with 16s DNA sequences?
I have 16S DNA sequences from diversity sequencing, and want to query these against NCBI's 16S rRNA database. If I ultimately want to get taxids for the species that my sequences have, does it make a ...
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1answer
80 views
Retrieval of genomic position by using biomaRt package
I have a list of several protein names, their primary gene name and their amino acid sequence (as extracted from the 'SEQRES' section in their corresponding PDB files).
I'm looking for the genomic ...
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1answer
58 views
How to QC overamplified shotgun library?
I made some NEB ultra II whole-genome shotgun libraries with around ~200ng of template going into the indexing PCR step. The PCR was run for 13 cycles and I ended up having high library concentrations ...
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2answers
780 views
Can I stop my nanopore sequencing run if there are no more reads being produced?
I am sequencing a whole genome on MinION. I have used this flow cell for 6 hours for the phage lambda control. That gave me around 300,000 reads. I started a 48h sequencing run on the same flow cell ...
