Questions tagged [alignment]
These questions are about sequence alignment.
152
questions
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26 views
Why do I get cytosine to guanine/adenine transitions in bisulphite treated sequences?
I got my sequencing results (bisulphite treated and non treated sequences of same species Allium cepa) and now I have to do analysis in Cymate online tool. I prepared all sequences as it is written in ...
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3answers
41 views
What programs account for structural alignment of different parts of distant homologs which have significant structural differences?
If there is a need to perform structural alignment of different parts of distant homologs, which program one should use?
Since distant homologs often have significant structural changes, meaning the ...
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0answers
27 views
BAM file filteing to remain best isoform
I ran HiSat2, MarkDuplicate, removed reads with the lower quality score than 40 and finally only kept properly paired reads.
After the BAM filtering steps, I used the Scallop results with TransDecoder....
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1answer
12 views
Installation of PRANK MSA in WLS Ubuntu 20.04 LTS
I want to install PRANK on the Windows 10 Linux subsystem (Ubuntu 20.04 LTS), I have followed the installation instructions to no avail.
...
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1answer
90 views
why in RNA seq don't we only use reference transcriptome?
I would like to ask why in RNA seq analysis (alignment step) we use sometimes reference genome instead of reference transcriptome? thank you!
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0answers
18 views
What are the symbols of $*$ and '$\_$' in an unknown alignment format for HLA data from the IMGT dataset?
Has anyone worked with the IMGT HLA database/dataset before? IMGT-HLA git repo they have some convenient text files (eg. link to gene A .txt file) with the genomic data for the different alleles of ...
3
votes
1answer
88 views
Difference between genome assembly and genome sequence alignment to a reference to find structural variants
I'm trying to determine what the difference and benefits of genome assembly and genome sequence alignments are when trying to identify structural variants or transposons in populations.
I've been ...
0
votes
1answer
30 views
Display a score or graph to visualize the degree of conservation of each residue from alignment data
I would like to display a score or graph to visualize the degree of conservation of each residue from the amino acid alignment data.
If possible, I'd like to extract the parts of the game that scored ...
2
votes
1answer
94 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 ...
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1answer
55 views
2
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1answer
20 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
votes
1answer
47 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'...
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1answer
38 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
48 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
vote
1answer
28 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 "/...
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0answers
39 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
vote
1answer
41 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
votes
1answer
28 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 ...
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2answers
52 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:
...
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0answers
34 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
votes
1answer
52 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
...
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0answers
27 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
vote
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
vote
1answer
20 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
votes
3answers
80 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
58 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 ...
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1answer
48 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 ...
4
votes
0answers
51 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
vote
3answers
57 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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0answers
94 views
bedtools coverage - Report the depth at each position in each A feature
I am using bedtools coverage to compute the sequencing depth at every positions of a chromosome but it didn't work as I expected.
Instead 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
votes
2answers
220 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
84 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
85 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
vote
1answer
94 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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vote
2answers
95 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
234 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
votes
1answer
83 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
23 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
64 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 ...
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0answers
68 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
votes
1answer
554 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
votes
2answers
1k 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
votes
2answers
98 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
...
3
votes
0answers
40 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
46 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
64 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
189 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 ...
