Questions tagged [alignment]

These questions are about sequence alignment.

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2
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0answers
35 views

Is there a modern alignment tool tailored for transmembrane regions?

I am looking for a project or tool that allows programmatic pairwise alignments of proteins but that takes care with transmembrane regions of proteins. TM regions are traditionally too information ...
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3answers
42 views

Is BWT based aligner suitable for any types of alignment task?

Burrows wheeler transformation based aligner like BWA or bowtie seems a standard alignment tool used many area. I was just wondering if there is a kind of alignment task in which BWT algorithm is not ...
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43 views

bedtools coverage - Report the depth at each position in each A feature

I am trying to use bedtools coverage to compute the sequencing depth at every positions of a chromosome but it didn't work as I expected. It reported 0 coverage at every positions. This is how I did ...
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21 views

What would the ratio of transitions to tranversions be in the Kimura model to equal to Jukes Cantor

I was thinking maybe a 2:1 ratio assuming that nucleotide frequencies remain the same for jukes. But if 2:1 then ln(1-2q-p) could go to 0 with that ratio and approach infinity
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2answers
33 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: ...
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1answer
39 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 ...
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1answer
37 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 ...
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1answer
61 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
44 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: ...
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2answers
148 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
68 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
17 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. ...
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1answer
43 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 ...
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3answers
83 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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47 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
148 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 ...
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2answers
324 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
53 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 ...
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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 ...
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2answers
40 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
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1answer
52 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
156 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 ...
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1answer
394 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
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1answer
82 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 ...
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2answers
418 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? ...
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0answers
150 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 ...
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3answers
96 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
32 views

Determining Read Groups

Which Read Groups are correct: ...
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3answers
737 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 ...
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0answers
70 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
168 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
133 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 ...
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6answers
362 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
97 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....
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2answers
561 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
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1answer
179 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 ...
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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
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1answer
220 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
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3answers
353 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
96 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
115 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 ...
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1answer
93 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 ...
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0answers
77 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
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2answers
243 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
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1answer
225 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
104 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
81 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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0answers
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
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1answer
91 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 ...