Questions tagged [read-mapping]
When dealing with associating sequencing reads to a matching position in a set of reference sequences (typically a genome).
57
questions
1
vote
1answer
17 views
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 ...
0
votes
0answers
38 views
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,
...
2
votes
1answer
58 views
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 ...
2
votes
2answers
49 views
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 ...
2
votes
0answers
21 views
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 ...
0
votes
1answer
111 views
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 ...
2
votes
1answer
44 views
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 ...
2
votes
0answers
58 views
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 ...
4
votes
1answer
66 views
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 ...
1
vote
1answer
50 views
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, ...
2
votes
0answers
47 views
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 ...
6
votes
2answers
279 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?
1
vote
1answer
108 views
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
...
2
votes
2answers
47 views
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 ...
0
votes
0answers
32 views
What Ensembl genome version of wheat should I use for alignments? [duplicate]
There are many genome files available from Ensembl. Which one is the best to use/download for wheat RNA seq differential gene expression analysis? Also, tell me which tool or aligner or mapper to use? ...
8
votes
1answer
74 views
Highly heterozygous reads mapping
I have short (67bp) Hi-C reads from a highly heterozygous organism (~15% between-haplotype SNP divergence) and I have both reference haplotypes.
I wanted to try and compare different haplotyping ...
5
votes
2answers
64 views
Control width of samtools tview “snapshot” when redirecting
I have a large number of loci I would like to examine manually with samtools tview. Rather than typing or copy-n-pasting dozens of coordinates, I was hoping to ...
2
votes
2answers
456 views
How to count the number of mapped read in 100-bp window from a BAM/SAM file
Although I know how to get total number of mapped read using samtools flagstat (samtools flagstat file_sorted.bam) but I want to count total number of mapped read ...
7
votes
2answers
280 views
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 ...
2
votes
0answers
37 views
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 (...
1
vote
3answers
160 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 ...
3
votes
1answer
90 views
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.
...
1
vote
0answers
19 views
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,...
6
votes
1answer
553 views
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....
1
vote
1answer
30 views
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.:
...
4
votes
1answer
77 views
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 ...
2
votes
3answers
81 views
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 ...
5
votes
2answers
317 views
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. ...
2
votes
2answers
70 views
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: ...
3
votes
1answer
510 views
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:
...
3
votes
1answer
1k views
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 ...
3
votes
1answer
635 views
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 ...
1
vote
2answers
40 views
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 ...
1
vote
2answers
354 views
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 ...
6
votes
1answer
497 views
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 ...
5
votes
4answers
2k views
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)...
5
votes
1answer
529 views
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 ...
5
votes
2answers
128 views
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) ...
11
votes
2answers
4k views
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 ...
4
votes
2answers
434 views
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 ...
4
votes
1answer
60 views
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 ...
3
votes
1answer
830 views
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 ...
1
vote
4answers
167 views
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 ...
4
votes
3answers
176 views
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 ...
6
votes
3answers
160 views
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 ...
7
votes
1answer
83 views
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 ...
5
votes
2answers
185 views
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 ...
9
votes
3answers
296 views
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 ...
5
votes
1answer
690 views
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 ...
11
votes
4answers
359 views
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. ...
