Questions tagged [read-mapping]

When dealing with associating sequencing reads to a matching position in a set of reference sequences (typically a genome).

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Is it normal to have low mapping to bacterial genome in a total RNA sample of plant root-colonized bacterial cells?

I had isolated the total RNA from a sample of plant roots with colonized bacteria by excising the roots (harboring the bacterial cells) and crushing them into a powder using liquid nitrogen. The RNA ...
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How to know if FASTQ/BAM is from reference genome (FASTA)?

I'm new to bioinformatics. I have a problem in which I have a FASTA reference genome and lots of reads in FASTQ files. Some of them could be contaminants, so I'd like to filter them out and get only ...
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Featurecount output .txt file from bam file

After running this command: featureCounts -p -s 2 -a $genome -o $dir"/"$specie"/count_table/"$value".txt" $output_loc -T 8 on the BAM output of ...
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Parameter optimisation of minimap2

I'm leveraging minimap2 to map select genes from short-read microbial fastq metagenomics zip files. ...
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Mapping List of Probes/Primers/Short Oligos to a Reference Fasta/q

Could you help me bioinformatics SE people. So I have been duckduckgo-ing up a storm and even consulted the AI overlords and haven't come up with a solid way to do this, but it is so fundamental to ...
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Reference genome (bwa -mem)

I want to do mapping with bwa mem. I downloaded a reference genome from ncbi database which is (Danaus plexippus). I got one ncbi_database.zip file which contain 2 ...
Moon's user avatar
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Mapping statistics from the bam files

I would like to find the mapping statistics from the sorted bam files. Samtools flagstat gives the output only for a single file. What is the easiest way to find the mapping statistics for all ...
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mapping nucleotide sequences

I am trying to do mapping with multiple sequences against a reference genome. I tried the following code: The outputfile is .fastq.sam. I need only .sam. How do I get it? ...
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Kallisto error: index input file could not be opened!

I am utilizing Kallisto in Anaconda/miniconda for RNA sequencing. I have successfully made ...
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Nextflow with Minimap2 not working

I'm trying to create a Nextflow script that maps assemblies to reference gene sequences. This is what I have so far: ...
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How do I generate a variant list using Illumina reads from a Salmonella genome?

I am planning on performing phylogenetic analysis of Salmonella specimens using WGS data from PulseNet and GenomeTrakr, for the purpose of public health surveillance & to provide context for ...
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Understanding PAF format

Does anyone have any experience with PAF files (minimap2 output)? I don’t fully understand what my output means. I’ve looked at the minimap2 explanation (https://github.com/lh3/miniasm/blob/master/PAF....
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Coordinate numbering between forward (+) and reverse (-) strand in Tombo

My question is related to the output of Tombo re-squiggling algorithm on nanopore data. Given the position/coordinate on one strand (+ or -), I want to find the coordinate of its exact location on the ...
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MAGs transcriptomics pipeline question

I have currently a following problem. I have a one sample that I did my metagenomics on (Illumina shotgun + nanopore) and have recovered some high quality MAGs. I also did a metatranscriptomics on the ...
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how to retain reads with low mapping quality (MAPQ) scores when using samtools view -q

I have been using the -q option of samtools view to filter out reads whose mapping quality (MAPQ) scores are below a given ...
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Get number of reads with a single, (almost) exact match to the full length of a reference sequence

I can't find an answer to this in previous questions, so hoping someone can help me now. We have nanopore sequenced a PCR product, and I've filtered our reads to +/- 10 bp of the expected product ...
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What tool I can use to map short-reads sequences to reference genome and get specific mapped size

I have about 300 90-bp sequences which I would like to map to a reference genome to make it longer to a 300bp sequence, wherein the 90bp is at the middle. Anyone knows what bioinformatics tool I can ...
Umi Rayearth's user avatar
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Low mapping reads for RNA sequence

I am new to RNA sequencing analysis. I have RNA samples for bacteria for different treatment. I did contaminant filtration, remove adapters and checked fastQC report: attached below for one sample (...
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using Bowtie to map miRNA-seq data to rfam and also reference genome

I am using Bowtie to remove non-coding RNAs (tRNA, snRNA, rRNA) by rfam and also maping our microRNA-seq data with mirbase using following code: ...
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Solutions to reference bias issue

I've recently learned about the reference bias issue - inability to properly map NGS reads in certain genomic regions caused by the fact that our standard genomic references are linear and do not ...
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What is the meaning of split read?

I want to use rna seq data to later perform functional tests on fusion genes. so before that I need to filter the "best results" (of rnaseq) for deciding which candidates I actually want to ...
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Modeling number of reads mapped to a gene

I am looking for a probability distribution of a number of reads mapped to a particular gene in metagenomic sequencing (NGS, shotgun, likely illumina). Naively one could model it via a binomial (or ...
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How to check what software has been used to generate bam file?

I have several bam files from unknown origin. I'd like to know what software was used to obtain those bam files, e.g. bwa-mem. Is it possible to somehow check it?
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Quantify low complexity regions in DNA sequences

I have fasta files with multiple sequences. They are reads that mapped to the genome outside of probe-targeted regions. From a quick perusal, they appear to be repetitive and have low complexity. Is ...
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How to rename Read Groups

I periodically run into problems with Read Groups. I am in a desperate need for a tool that would allow me to fix them. This time, when I was mapping reads, I formatted all the information in the Read ...
Kamil S Jaron's user avatar
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What is "unmapped read segments" in the output of samtools idxstats?

samtools idxstats produces a four column output (see here) ...
Roger V.'s user avatar
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Reads count in metagenomics

Background: I am developing a pipeline for metagenomic studies of human gut microbiote. In particular, I am mapping the reads data originating from shotgun whole genome sequencing onto a gene ...
Roger V.'s user avatar
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How to control/normalize for number of reads when calling SNPs using RNA-Seq?

I used the GATK pipeline to call SNPs on males and females using RNA-Seq data. But the males have a higher read count (~43-46M reads) than the females (~40-42M reads). This causes SNP counts to be ...
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Contamination on genome assembly

I had a question for the community. I have a genome of a new species that has been sequenced via 150pb Illumina paired-end. To verify the quality of the assembly I used the ...
chippycentra's user avatar
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Difference between paired-end, mate-pair and long read

I writing here because I have some questions for you. I wondered what the essential differences were between paired-end, ...
chippycentra's user avatar
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Question: Bismark methylation for non-uniquely mapping BS-seq reads

I am looking for the DNA methylation, specifically inside small RNAs; piRNA. I am mapping BS-seq reads on the genome with bismark. From the user guide of bismark, it maps reads uniquely on the genome, ...
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Assemble reads for a specific gene

I have a lot of unassembled sequencing data and I want to build phylogeny for some genes from these data. I can retrieved the sequene by mapping reads to a reference sequence but if the two species ...
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How do you map nanopore fast5 files?

Is there a best practices for mapping Oxford Nanopore files to a reference? Is there a tool that can take a tarball of fast5 files and map them directly or do they need to be converted to fastq first?...
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How to choose reference to calculate coverage of WGS of organism that has high intra-species variation?

Calculation of coverage involves mapping reads with a reference and depending on the choice of reference we can get very different result. If a species has a genome that has very low size variation ...
Ahmed Abdullah's user avatar
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2 answers
2k views

Error with BWA Mem input having multiple fastq files using cat and process substitution

Running BWA Mem on a number of paired end fastq files using process substitution on the inputs results in this error: ...
111's user avatar
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What do the symbols mean in minimap2's gap cost equation?

Heng Li's paper on minimap2 is understandable to me right up until the moment that it gives this definition of gap cost: 2.2.1 Alignment with 2-piece affine gap cost Minimap2 performs DP-based ...
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How to obtain the extended unaligned bases of the read in reference based genome assembly?

I did illumina read mapping based on a particular gene sequence (reference sequence) using the following command, ...
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Oxford Nanopore mapping Quality and sequencing error

I'm analyzing some Oxford Nanopore sequencing reads, with several articles stating the sequencing error is between 5% and 15%. Since its 1D and not 1D^2 sequencing i would assume the sequencing error ...
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Patient-sample mapping in GSE72056 dataset

I want to use the single-cell data from the following expression profiling which concerns the RNA-seq of metastatic melanoma: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE72056 The data was ...
hadi's user avatar
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2 answers
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How can I transform a mapped BAM file into an unmapped BAM file?

In order to use MergeBamAlignment (Picard), I need an unmapped BAM file and a mapped BAM file. I have two mapped BAM files: one with reads mapped to the reference I want but without metadata such as ...
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RNASeq read coverage in protein space?

I used samtools depth to find the per base-pair read coverage over a number of isoform contigs from my Trinity assembly. I have also conducted a multiple sequence ...
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bowtie2 options when mapping stranded single end reads

I'm trying to map RNA-Seq reads generated using the NEB Ultra Directional kit is first strand reversed protocal. I'm using bowtie-2.3.5_1 to align against the mus ...
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2 votes
1 answer
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No refseq transcripts in 2nd half of Y chromosome for HG38

Obviously there is a gap in my understanding of how sex chromosomes are annotated. I've been working on some CNV calls and noticed that most of the 2nd half of ChrY is missing annotations and no reads ...
111's user avatar
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Merging/concatenating index files

I was wondering if any one has had success merging pre-generated reference index files for BWA, bowtie2 from multiple references? For a concrete example I have hg19 and a bunch of viral and ...
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Displaying soft-clipped nucleotides in samtools tview

There are nicer genomics visualization tools available, but the samtools tview command is almost always my go-to for a quick first look at read alignments. I just ...
Daniel Standage's user avatar
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1 answer
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Batch alignment of inconsistently named Fastq files

I have numerous gzip-compressed paired-end Fastq files with ChIP-seq data that I would like to align with bowtie2. I confirmed that bowtie2 takes .gz files, ...
kcm's user avatar
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How snippy makes MSA-like aligned fasta output from multiple samples?

From the log file it seems snippy doesn't do assembly. It only does mapping: fastq --> SAM --> BAM --> VCF --> consensus_seq/snps But if multiple ...
Ahmed Abdullah's user avatar
7 votes
2 answers
3k views

Definition of "seed" in sequence alignment

I would like to know what is meant by "seed" for various sequence aligners. How is it important?
user3138373's user avatar
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1 answer
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HISAT2 - are all multi mapped reads reported by default?

While going through the HISAT2 manual, one can see this: Two alignments for the same individual read are "distinct" if they map the same read to different places. Specifically, we say that two ...
Siddharth's user avatar
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bedtools: get name column of alignment file A

I'm using the coverage function of bedtools to check whether a certain set of regions (file B) has any overlap with known ...
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