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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What is mate rescue in bwa mem?
BWA mem has the -S and -P tags for skip mate rescue and skip pairing; mate rescue performed unless -S also in use.
What do ...
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Calculating alignment/mapping time
I am trying to assemble a plant genome using AWS resources using velvet. Plant genome is huge (> 10 times human genome) and coverage is around 30 x. We are planning for de novo assembly with Velvet (...
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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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Problem: "Pair-end" reads scRNA seq data (Drop-seq)
In case of Drop-seq, we have paired end data.
Read 1: Cell code + UMI (unique molecule identifier)
Read 2: The transcript information
But I have a problem/doubt with the sample I am working on.
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Visual representation of detecting deletion by different read types
I'm having some trouble differentiating between CNV, split reads and read pairs and how each one elucidates the presence of a structural variation, say deletion.
Given a reference and donor sequence,...
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What are "split reads" and "intron clusters?"
I'm working through the example data set for LeafCutter and the documentation mentions "split reads":
This will cluster together the introns fond [sic] in the junc files listed
in test_juncfiles....
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Does read sequence identifier need to be unique for proper alignment?
I am preprocessing a set of scTHSSeq reads in which each read sequence identifier has been replaced with the cell barcode, e.g.:
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Reference genome for allele specific expression
We are trying to sort out a pipeline for doing allele specific expression. Our plan is to call SNPs from RNA-seq data and combine with known SNP annotations. A well known problem in ASE is reference ...
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How to detect mismatch before mapping in RNA-Seq data
In the methods of this paper, the authors say:
Reads were then filtered based on quality score in the UMI region. Any read with >1 low-quality base (phred <=10) were discarded. Reads with more ...
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What is the correct way to map Hi-C data with bwa mem?
Library Prep
I have a Hi-C library prepped using an enzyme that cuts at GATC, so it leaves GATCGATC as the junction sequences. ...
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How to map reads shorter than 32bp with minimap2?
I mapped fasta sequences to a reference. The fasta sequences range in length from 17bp up to several hundred bp. I used minimap2 with the following command: ...
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Can I run STAR without an annotation file?
I wish to use Rascaf to scaffold a fragmented draft genome.
For this, I need to provide a BAM file of aligned RNA-seq reads and the draft genome.
So, I indexed the draft genome with STAR like this:
<...
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Hisat2 : which option should mention for strand specific library read
I was trying hisat2 I get confused by the strand options...
The question has been already asked on github here but didn't get any satisfactory answer.
I'm surprise how much this strand information ...
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Strange per sequence GC content results
I would be grateful if someone could take a quick look at these FASTQC results. This is rna-seq paired-end data. From the FASTQC manual, an unusual distribution seems to be suggestive of contamination ...
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Mapping bisulfite reads to a reduced size genome
Is it worth mapping bisulfite reads (WGBS) to a reduced size genome?
I'm interested only in modifications in CpG context, thus instead of mapping to a whole genome (human genome) I would:
Extract ...
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Mapping Information from SAM/BAM file
I mapped raw illumina reads to longer pacbio reads and I would like to know the following information from my mapping file (SAM/BAM)
How many PacBio reads are mapped to at least one illumina reads
A ...
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How to trim adapter sequences from GSE65360 in order to map the reads?
I am trying to map single-cell chromatin accessibility data from doi:10.1038/nature14590, obtained using scATAC-seq, to the reference genome. Example paired-end reads are here.
The reads contain ...
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Why total RNA-seq usually yields low mapping rate?
Maybe this is a silly question, but I'm really wondering why we usually get low mapping rates if we map total RNA-seq, but not poly(A)-enriched (in particular, for human, mouse, and zebrafish datasets)...
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What is local realignment and what is the problem it solves?
I am trying to understand local realignment but I could not get a clear idea of what is the problem solved by it.
For example, reading Homer and Nelson (2010):
Because alignment algorithms map ...
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RapMap: reference transcriptome for simulated reads
I am very new to bioinformatics and trying to repeat the benchmark in the RapMap paper with an experimental tool working in a similar but different fashion.
In the paper (taken from their github) ...
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Meaning of BWA-MEM MAPQ scores
Does anyone know what the MAPQ values produced by BWA-MEM mean?
I'm looking for something similar to what Keith Bradnam ...
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Problems to Extract uniquely mapping reads from BWA MEM alignment
I did a mapping of genomic paired-end reads to a reference assembly using bwa mem. I need to extract the reads that mapped only once to my reference.
For that, I have tried to follow the method ...
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Best way to detect long insertions in bisulfite sequencing data?
I am interested in identifying indels in whole genome bisulfite sequencing data (76bp paired end). Currently, I do this by setting the -rfg and ...
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Counts obtained by featureCounts seem much less than observed coverage
I have surprisingly low counts when running featureCounts on some (single-end) RNA-seq data mapped on C. elegans genome using ...
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At what processing step should library strandedness type be taken into account?
Suppose I have single-end RNA-seq data for which the reads in the fastq file are reversed with respect to the original extracted RNAs.
Suppose I have the following workflow:
Map the reads on the ...
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what percentage of the human genome is MAPQ=0?
When doing Illumina 2x150bp sequencing of genomic DNA, and after aligning the reads to GRCh38, what percentage of the non-N fraction of the human genome is MAPQ=0? This is, what part corresponds to ...
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Filter Trinity transcriptome based on RNASeq reads
I have recently generated a genome-guided transcriptome with Trinity, and would like to apply an additional filter to exclude transcripts that don't have good support from the RNASeq reads. This is ...
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How to interpret contig-alignment.psa produced by velvet
I'm using velvet to align given reads of RNA to given CDSs (i.e. coding areas and genes) of an organism, so I can generate gene-expression profiles. But after using ...
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How to estimate whether a long-read is meaningful sequence?
The setup
Imagine that I work on an organism without a reference genome, and that the closest reference genome I can get is quite diverged. E.g. ~10% diverged in terms of SNVs when measured with ...
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Visualisation of long read RNA-Seq splicing
I have a dataset of Oxford Nanopore cDNA reads. Many of my reads are full-length or close to full-length transcripts, and I and am interested in examining alternative splicing. For this, I would like ...
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How do I generate a variant list (i.e. VCF file) using Illumina reads from a human genome?
This is a problem I have to solve frequently, and I'd be interested in knowing what other methods people use to solve the same problem.
About twice a year, I get asked to determine variants from ...
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Library for computing BWT-based alignments
I am writing a software tool to which I would like to add the ability to compute alignments using the efficient Burrows-Wheeler Transform (BWT) approach made popular by tools such as BWA and Bowtie. ...
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Accidental mapping of eukaryotic reads in a metagenomic dataset
This is a question from /u/wipeyourmit on reddit. The original post can be found here.
If I have a metagenomic dataset that contains reads from both
eukaryotes and prokaryotes and then I annotate ...
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What is the difference between SAM mapping quality and Blast E-value?
Blast reports E-values, but short-read mappers report mapping qualities. Are they the same thing? Can they be converted to each other? If not, why blast doesn't report mapping quality while short-read ...
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Why is bwa-mem the standard algorithm when using bwa?
The industry standard for aligning short reads seems to be bwa-mem. However, in my tests I have seen that using bwa backtrack (bwa-aln + bwa-sampe + bwa-samse) performs better. It is slightly slower, ...
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Which reference to use for read mapping for popular model organisms
What is the "best" assembly for the popular model organisms:
human (GRCh37 and GRCh38 are obvious, I'd pick whatever bwakit uses)
mouse (GRCm37/GRCm38, OK)
but what about non-human/mouse ones?
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Why is SMALT better for microbial genomics than other mappers?
SMALT seems to be one of the most used read mappers for bacterial data, see, e.g., this query. I do not say that it is not a great mapper, but I cannot easily see what are its main strengths compared ...
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How does the BWA-MEM algorithm assign its mapping qualities?
Is there any resource (paper, blogpost, Github gist, etc.) describing the BWA-MEM algorithm for assigning mapping qualities? I vaguely remember that I have somewhere seen a formula for SE reads, which ...
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Difference between BWA-backtrack and BWA-MEM
Many of my colleagues recommend I use BWA-MEM instead of regular old BWA. The problem is I don't understand why and reading the BWA man page doesn't seem to help the matter.
What is the difference ...
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