Questions tagged [alignment]
These questions are about sequence alignment.
120
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1answer
25 views
BED file from .bam alignment structure
I am using a pipeline from nanopore to detect structural variants (SVs) in a human sample with long-reads sequencing. The first steps of the pipeline are:
index the reference genome with ...
1
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1answer
32 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 ...
1
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1answer
51 views
Read alignment using Bowtie2
So this is related to CRISPR-CAS9. I am working with off-target predictions for my thesis and was looking at all scientific papers related to CRISPR. I found one and decided to use their datasets. The ...
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2answers
33 views
MiXCR: only create a single export file for all clonotypes
I am using following command from MiXCR to both align, assemble and export my input files:
...
1
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2answers
136 views
How can I find out if my gene of interest is duplicated?
To identify homologous genes, I performed tBLASTn analyses against my genome of interest resulting in sequences of a closely related species. Using this method, I found two (and in some cases up to ...
2
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1answer
66 views
Appropriate tool or algorithm for sloppy alignment of degenerate bases
I have an optimization problem where I have a degenerate nucleotide sequence I want to align against subsets of a reference genome (exons, specifically, to make the problem more tractable).
The ...
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0answers
16 views
How to build ML tree among OTUs and 16s sequence
I have OTUs sequence generated from 16s V4 clean reads, and want to build maximum likelhood tree with selcted taxonomy 16s refseq from Sliva database.
...
2
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1answer
41 views
For phylogenetic tree construction from core-genome which one is preferable: amino-acid based MSA or nucleotide based MSA?
The genomes are from same species.
Is it true that, in phylogenetic tree constructed from amino-acid based MSA (multiple sequence alignment) some information are lost, so for phylogenetic ...
3
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3answers
82 views
Compare multiple alignment results' aligned bases
I have aligned a nanopore data set to a reference genome with graphmap, minimap2 and BLASR. The alignment results are stored in BAM files.
I would like to do some concordance assessment, looking at ...
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46 views
How should I deal with segmental duplications when aligning NGS reads to a reference genome?
This is a follow-up of my other question. I have been having trouble calling variants in the human SMN1 and SMN2 genes, because the human genome has a large segmental duplication there and these two ...
3
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1answer
93 views
What do the read colors in IGV mean?
I was looking at a bam file in the IGV viewer and saw:
What do the different read colors mean? Why is one read a light blue color, another green, another aquamarine (?), another purple and another ...
2
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2answers
176 views
Error while calling bcftools mpileup - Failed to open -: unknown file type
I have sequenced a bacterial genome with a GridIon from ONT. Basically what I want to check is whether or not trimming 50 bps at the beginning of the reads will improve alignment against the reference ...
2
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2answers
46 views
Error: sort order of reads in BAMs must be the same
I am a novice to bioinformatics trying to run a cuffdiff job in cufflinks and keep getting this error message:
Error: sort order of reads in BAMs must be the same
...
2
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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 ...
1
vote
2answers
38 views
Global or local alignment on sequences for which it is assumed that they have common ancestry
As the title says I would like to know which alignment method(global or local) should I use for sequences for which is assumed that they have common ancestry?
The sequences are 21 aa long peptide ...
2
votes
1answer
51 views
Alignment for predicting DNA hybridization?
I am currently working on a Computer Science project where we are trying to build a large set of orthogonal single-stranded DNA sequences. The goal would be to ensure that when put in solution, the ...
2
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2answers
145 views
Frequency of specific viral sequence in .BAM or .fastq
I was wondering if anyone had any experience 'counting' the frequency of a particular viral sequence in an individual's fastq sequence. So basically, counting the number of occurrences of a particular ...
2
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1answer
302 views
How do I find split reads?
How can I detect a split read in a BAM file?
Is there any sign in the CIGAR string that describes split read?
3
votes
1answer
73 views
Pipeline for extracting gene from multiple genomes for use in HyPhy selection analyses?
I have been trying to obtain some preliminary data from HyPhy selection analyses to inform a larger project. I have obtained a number of assembled mammalian genomes from NCBI with the initial goal of ...
6
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2answers
297 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?
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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? ...
1
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0answers
119 views
Aligning nucleotide sequences in APE software
I am very new to APE software. I am trying to align complementary oligo-DNA strands using APE on macOS. I have both the forward and reverse sequence of an oligo-DNA insert in two separate files. But I ...
3
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3answers
86 views
Alignment with arbitrary number of mismatches or gaps
I have 23bp long reads and want to find all possible alignments of them to the human genome (hg19, hg38) for an arbitrary number of mismatches (<7), possibly also small indels. I've read in ...
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1answer
31 views
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607 views
How to get fasta alignment file from SAM/BAM file?
I am not talking about consensus sequence, I know how to get consensus sequence using mpileup in samtools/bcftools. As I understand , SAM/BAM files are basically sequence alignment format so it's ...
3
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0answers
65 views
convert supplementary reads to primary in sam or bam
I have a problem with a tool, that possibly ignores supplementary reads. I want to find out a bit how this tool works by converting all supplementary reads to primary reads, and then change the names ...
4
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1answer
160 views
Can blat use more than one core/CPU to speed up the alignment?
I am using BLAT to align two versions of the genome of C. elegans. I can see in the Activity Monitor of my Mac Book Pro High Sierra that blat is using 100% of a CPU....
3
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1answer
88 views
Multiple sequence pairwise global alignment against reference sequence
Background
I have a fasta file with protein sequences. The first sequence in the fasta file is the reference sequence and every subsequent sequence is something I want to align to the reference. The ...
5
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6answers
289 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 ...
5
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1answer
91 views
Why is a PacBio read length larger than the aligned reference region?
I recently had some Iso-Seq sequencing done on my organism catfish on the new Sequel platform and got weird alignments for a size selected 4 Kilobase and up fraction after running the isoseq3 pipeline....
2
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2answers
462 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 ...
5
votes
1answer
149 views
How to output all sequences with bwa mem, not `*`?
I've been running bwa mem -a for alignment, using the -a flag---this will
output all alignments for SE or unpaired PE
I've ...
1
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0answers
13 views
Finding the conserved region of protein in a given set of Kingdom
We have to find the conserved region of proteins in a given set of kingdom and we have to give more weightage to distantly related organism. What approach I should take to solve this problem?
5
votes
1answer
168 views
Does the “.full.aln” file produced by snippy-core contain all bases of my input sequences aligned to the reference genome?
I have a number of sequences and a reference genome. I used snippy to align each individual sequence with the reference genome. I then used ...
5
votes
3answers
322 views
Total reads aligning to each reference within a bam file
I have two PCR amplicons that have been multiplexed and sequenced using the nanopore minion.
I have aligned the fastq reads using minimap2 with a reference file containing both amplicon sequences and ...
3
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1answer
81 views
cDNA and alignment mapping
I am confused with RNA seq alignment. My understanding is that after Mature mRNA is isolated from the cell, it is then fragmented and using reverse transcriptase enzyme a cDNA copy is created which is ...
4
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2answers
106 views
How to align output of grep --color=always? (To QC fasta/fastq files)
Grepping out short sequences from a fasta or fastq file is a really useful way to look at sequencing data. Using the option --color=always makes this even more ...
0
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1answer
86 views
How to calculate Gene Ontology terms in python
I am testing different Protein-Protein Interaction networks alignment tools. I observed that all alignment tools show some ...
3
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0answers
67 views
How to assign the best gap penalty and gap extension penalty using BLOSUM65
For an assignment I must do a pairwise optimal local alignment using BLOSUM65 and five protein sequences. The algorithm I want to use is the Smith-Waterman.
Context protein sequencing using Blastp: ...
6
votes
2answers
241 views
Sequence alignment using Markov Model
I am learning about applying Markov model to sequence alignment. The prof says that the transition probabilities from a gap-residue alignment to a residue-gap alignment and vice versa are both 0. Is ...
4
votes
1answer
210 views
How to map short sequences to long reads, recovering all multiply-mapped high-quality matches
The dilemma:
I have a problem where I have around one million short sequences (21 bp to several 100s of basepairs) for which I need to identify all occurrences of in 20-30x coverage noisy long reads (...
5
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2answers
100 views
Counting letters in phylip alignment columns with Biopython
I have been using python 3.6 and biopython 1.72 to work with protein data files. I am using a protein sequence file (phylip format), for example:
...
4
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1answer
77 views
Efficiently aligning a lot of reads on the same small reference sequence
The context: I have a DNA-sequence coding for a protein, about 1500 bp in length. Using NGS, a lot of reads of (mutants of) this same sequence were acquired. All of these reads need to be aligned to ...
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26 views
Stand alone chaining tool for existing blast hits?
I have a table of blast hits in a database that I'd like to chain. What is a good choice for a 'stand alone' chaining tool? Is it simple to implement in Perl, for example?
Example 'hit' data is here. ...
2
votes
1answer
83 views
Minimap2 -ax map-pb doesn't output tlen field
I have used minimap2 to map some pacbio reads to a reference genome. I would like to know the "insert size" (true length of sequence) relative to the reference. More specifically, I want to know the ...
3
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0answers
84 views
Glocal\semi-local\Hybride Globale-Local alignment with Python
I was looking for a simple way to do a glocal alignment.
The case I have is I have a small sequence which should be find in a bigger one, thus typically a glocal alignment.
Also I can not Install ...
0
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1answer
91 views
Find a map/correspondence between two versions of a genome
I am working with two versions of the C. elegans genome. I am finding interesting regions (specifically, tRNA genes) in version 1 and then I would like to know if version 2 also has a tRNA gene in ...
2
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0answers
26 views
Alignment using secondary and tertiary features of DNA
I m trying to align different sequences of length not greater than 50. Is there any way to incorporate other information such as stacking energy, entropy, bonds etc. If there any way to align ...
0
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1answer
124 views
GMAJ error: Exception in thread “main” java.lang.ClassCastException: java.lang.StringBuffer cannot be cast to java.lang.String
I have installed GMAJ using:
...
2
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1answer
307 views
pysam pileup: what reads appear in the pileup?
Cross-posted on Biostars (with no answers currently). I hope that's OK.
I thought that iff a read matches the reference at a position, it would appear in the pileup column for that position. But ...
