Questions tagged [alignment]

These questions are about sequence alignment.

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2
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1answer
46 views

How to extract unmatched reads using bwa and samtools?

I have a single read (NOT paired) that I need to pass through the workflow described in Beauclair et al. paper (free version here https://rnajournal.cshlp.org/content/24/10/1285.long) for identifying ...
0
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1answer
31 views

Can't align 2 sequences, (MAFFT killed)

I have 2 .fa sequenes like: ...
2
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1answer
18 views

which is the right prosite pattern?

I would like to ask if the right Prosite pattern for this multiple alignment: Is it this: A-T-[AT]-G-x-C-[AGC]-C-x(1,4)-A or this: ...
0
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1answer
43 views

How to calculate mutation rate and mutation sites in a genome using FASTA file?

I have 6 viral genome sequences of the same virus and 1 reference sequence in FASTA format. I want to know, how I can identify mutations and mutation sites in those genomes using FASTA sequences (If I'...
0
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1answer
37 views

How to change sequence format in my alignment file?

I have fasta file with alingned several sequences (from MUSCLE), when I open it (e.g. notepad++) they look like: And I want dot format of identities like and then save it in txt file. I failed ...
0
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1answer
43 views

Why use Needleman-Wunsch if there is no way to evaluate the statistical significance

I thought that Needleman-Wunsch is the best approach to align sequences. However, I read that it is impossible to evaluate the statistical significance of the alignment if you do global alignment. So ...
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0answers
15 views

Getting BLAST to show similar sequences outside of a specific protein family

I'm trying to build an alignment of proteins in the major facilitator superfamily (MFS). I have alignments of a family of peptide transporters, the SLC15 family, but I would now like to extend the ...
1
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1answer
23 views

marge the matrix from computematrix of deeptools

I have several matrix from computematrix of deeptools. I need to merge two of them using "computeMatrixOperations cbind -m input1.mat.gz input2.mat.gz -o output.mat.gz" but I am running to error "/...
1
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0answers
38 views

How can I interpret multiple alignment results?

I would like to ask how I can interpret objectively multiple alignment results. I have used JALVIEW and TCOFFEE. I would like to ask if consistency score plays any role in the interpretation? I ...
1
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1answer
35 views

What's the meaning of having different alignments with the same qname in a bam with no duplicates?

I have removed duplicates from my bam file (not secondary, nor suplementary alignments), and then I have looked for some repeated qnames (to assess the failure of a ...
3
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1answer
24 views

Chromosomal order of supplementary alignment in BAM file “SA” tag

I have several long-read sequences, which when aligned to a human reference genome, aligns to multiple chromosomal fragment as a result of chromothripsis shattering the linear DNA and randomly piecing ...
1
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2answers
46 views

Extract end position from CIGAR

I was wondering how could I obtain the end position of an alignment using its start position and its CIGAR String. If an alignment present some soft clipping, for example: ...
1
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0answers
33 views

Unmapping Alternative reads in BAM file

I want to do some HLA typing, most of the tools require the bam file is aligned to primary genome without alternative read handling. From the International Genome Sample Resource project, I can get ...
2
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1answer
43 views

Translating a genome sequence into possible frames

I have a sequence below from MYC gene about which I need to translate the sequence in all possible frames AND identify (for each frame) which codons are actually used in MYC ...
0
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0answers
26 views

Given a multiple sequence alignment, how do I output all of the non-consensus characters by location?

I have an MSA from MAFFT, and I would like to quantify the "variants" between these sequences. What is the standard tool to do something like this? I'm familiar with calculating an MSA, and then ...
1
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1answer
39 views

choosing a good representative genome subset

I'm trying to build a genomic database for DNA alignments. I started with NCBI accessions, but the data is very multiplicative, so I want to use subset of [max] N different strains for each specie. my ...
1
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1answer
17 views

Running tophat dockerfile in background

I need to use tophat2 to align some sequences, and I wish to use the docker container. These are large sequences so it will take a long time, plus I'm working on a university server so the chances of ...
2
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3answers
79 views

Make a fasta out of mapped reads without taking into account the reference

I've aligned reads onto an haploid reference genome. I'd like to have a consensus sequence of all my aligned reads that doesn't take into account the reference genome I used (i.e. I just want the ...
2
votes
1answer
50 views

How can I not show insertions in the Integrative Genome Viewer (IGV)?

I am using IGV 2.5.2 and would not like to see the insertions in my aligned reads. How can I do that? I have managed to remove mismatched bases because there is an option to do so when I right-click ...
0
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1answer
40 views

Use of Electronic Phenotype in EHR

May I know what's the use of Electronic Phenotyping using EHR data? I did refer this link but have few questions I understand that ...
3
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0answers
44 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 ...
1
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3answers
54 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 ...
1
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0answers
69 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 ...
0
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0answers
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
2
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2answers
151 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: ...
1
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1answer
71 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 ...
2
votes
1answer
65 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
91 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 ...
1
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2answers
88 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
212 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
79 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 ...
0
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0answers
22 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. ...
3
votes
1answer
60 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
votes
3answers
94 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 ...
0
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0answers
61 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
439 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
976 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
79 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
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2answers
44 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
59 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
votes
2answers
181 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
794 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
121 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
1k 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
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0answers
230 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
votes
3answers
135 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 ...
3
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1answer
65 views

Determining Read Groups

Which Read Groups are correct: ...
5
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3answers
1k 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
votes
0answers
91 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 ...