Questions tagged [sequence-analysis]

Umbrella term for understanding any given nucleic acid sequence code, either as a locus, loci or genome with itself or as a comparison to comparable nucleic acid sequence code either intraspecifically or interspecifically

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26 views

Multi Factor in Deseq2 Gene enrichment analysis

I want to see how the gene expression differs in breast cancer between three species, and I am using DESeqDataSetFromMatrix on my count table. ...
1 vote
1 answer
162 views

Arlequin files not able to converge beyond 2000 steps for some .arp files

I am looking at 59 mitochondrial CO1 DNA sequences of length 563bp, but it is a haplotype file and it has 9 haplotypes within. When I use .arp files in arlequin to run mismatch distribution it says ...
1 vote
1 answer
690 views

tensorflow nn_model for DNA sequences: Matrix size-incompatible: In[0]: [2,1], In[1]: [784,300]

Hope anyone can help a beginner here. I'm building a proof-of concept tensorflow classifier for DNA sequences. However, the NN model does not let through train and test vectors saying the matrix size ...
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2 answers
30 views

How to classify TF motifs by family

I have a FIMO output, the input sequences were putative promoter sequences of several species. I want to graph the positions of these motifs along a horizontal graph, but I want to filter the data by ...
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1 answer
73 views

Error while Importing fastq sequences to jMHC software

I am trying to analyze my .fastq files (MiSeq exon reads) with the jMHC software, but output files I have obtained have no results. I think I might be doing something wrong during the first step: "...
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Recommendations on Motif scoring functions

I am searching for specific transcription factor binding locations on DNA, and ranking them according the their scores. For this, I am in search of a tool or method that can generate motif scores for ...
3 votes
2 answers
3k views

Samtools sort: most efficient memory and thread settings for many samples on a cluster

We're preparing to analyze thousands of .bam files beginning with re-alignment, sorting, etc. Complicated question: Has anyone investigated the optimal thread and ...
3 votes
1 answer
53 views

probability of finding a 5 amino acids in a row within a proteome

How to calculate the probability of finding two proteins that share a 5 amino acid long motif from a proteome of around 1067 proteins that have an average length of 65 residues. The probability of a ...
2 votes
2 answers
41 views

Longstitch error make: command: Command not found *** No rule to make target

I installed Longstitch and ran the test script with no issues. The output files matched the expected output files. But when I am now trying to run Longstitch on my own data I am getting this error. <...
2 votes
1 answer
137 views

working with cutadapt

I'm working with ion torrent data where I apply the program cutadapt. I'm analyzing ITS seq data, as well as Matk. When I'm using cutadapt, I search the information for this genes, and built new ...
1 vote
0 answers
65 views

Bracken not working

I have some highly contaminated ancient DNA sequences. I have adapter removed and collapsed these and run them through Kraken2. The Kraken reports show multiple levels of taxa with good numbers of ...
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1 answer
149 views

How to use extractfeat?

I am working on a script on bash linux to get the CDS (coding sequence) of a gene using extractfeat by EMBOSS. It gives me the error: Warning: No sequences written to output file I am unsure if my ...
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1 answer
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What does the different sequences represent?

I am using this package nsdpy to download genome sequences from NCBI nucleotide database. Specifically I am interested in the whole mitochondrial genome of different species, here I will use a subset ...
3 votes
1 answer
169 views

Trimmomatic QC report shows drop in the reads and presence of overrepresented sequences

This question was also asked on Biostars I am performing a de novo genome assembly using Illumina paired-end short reads, sequenced on a NovaSeq X by our collaborator at UCLA. At present, I am in the ...
0 votes
1 answer
60 views

How to find amino acid sequence of a given protein

Is there a way to look up the amino acid sequence of a given protein? For example, what amino acids are used to produce Amylase? I spent hours googling but to no avail. If that's impossible, how can I ...
2 votes
1 answer
51 views

How to map list items which are in groups in the dictionary values and return keys corrosponding it?

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2 votes
2 answers
62 views

paired-end short reads: will one file suffice?

I have a quick question about paired-end short reads. I have multiple genomes that were sequenced with paired-end Illumina NextSeq 200 technology, resulting in two fastq files per sample: ...
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Finding mutations in glycosylation sites

We are going to look at the likely N- and O- glycosylation sites within MUC16 (Q8WXI7 · MUC16_HUMAN)§ by in house long-read DNA sequencing data (PacBio). Counting the number of tandem repeats is a ...
-1 votes
1 answer
54 views

Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length distributions?

Is there a data analysis software (free) or code that I can use to view normalized CDR3 amino acid length distributions? Regarding code, preferably using Python or R. EDIT: Added a picture of the non-...
2 votes
1 answer
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Is there a graphical/interactive 16S rRNA clustering method?

I've been doing phylogenetics with large (hundreds) 16S rRNA sequences lately. Usually I'm focusing on one order, and using a combination of trees and sequence similarity to assess stuff like 'is this ...
2 votes
2 answers
75 views

How can I run the fdnadist command from the EMBOSS package?

My operating system is Mac OS X. I would like to compute DNA distances between different sequences. For this, the dnadist package from the Phylip software would be good but hard to automate. EMBOSS ...
4 votes
2 answers
161 views

Motivation behind the neighbor-joining distance matrix recomputation

In each iteration of the neighbour-joining method of phylogenetic trees construction, after joining the nearest neighbours the (additive) distance matrix $D_{m \times m}$ is recomputed as $$Q_{ij} = (...
-1 votes
1 answer
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stats.sh error in BBmap package

I am trying to calculate the N50 value from the assembled FASTA file. I used stats.sh from the BBmap package. I executed the following command ...
2 votes
1 answer
126 views

Math on Pandas Columns

I have a pandas dataframe that reads in a PAF file from minimap2. What I would like to do is take the first 5 columns of the data from to create a BED file. I used this to extract the first 5 columns: ...
3 votes
2 answers
125 views

missed cleavages combinations generation

I am looking for an R based solution to the following problem: Trypsin does not cleave perfectly in proteomics experiments. So starting from a protein sequence FASTA I want to generate all possible ...
2 votes
2 answers
1k views

How to identify the DNA sequence of a gene in the complete genome sequence FASTA format file?

I need to identify the sequence of a gene in the complete genome sequence . I thought it was simple, instead it is not a straightforward task ! My method was the following: I downloaded the FASTA ...
0 votes
1 answer
113 views

How do I build the MinusB database for Kraken2? (Taxonomy issues)

I am attempting to build my own custom database for Kraken2. I have two questions: If I have the MCPyV genome in a file called MCPyV.fasta, how do I build a database with just this? How do I build ...
1 vote
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Can files with different R1 and R2 lengths be trusted?

I received paired end amplicon sequence from a LAB with different lengths for R1 (320) and R2(280). Should I trust this lab to sequence other samples? Also, I had to do a trimming over the R2 at 220(...
1 vote
1 answer
287 views

reverse translation from amino acid string to DNA strings

what is the opposite of .translate() function calls ? I mean let's say I am given an amino acid string CYCLIC, how do I obtain all the possible combinations of DNA ...
2 votes
2 answers
85 views

Multiple Alignment cost application

Is there any biological application/case where someone would be interested in the estimated total cost of the alignment between a set of sequences (genes or amino acids) without the aligned sequence ...
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1 answer
436 views

Fastqc- Per Base Sequence Quality

I am trying to figure out how to interpret the "Per Base Sequence Quality"? What does Position in reads (bp) mean? Also in order to draw this box-plot graphics, more than one quality scores are needed ...
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What statistical analysis should I perform on DNA variants from unequal number of case (34) and control (11) samples?

I have performed NGS on 34 patient samples and 11 controls. Now I have variants from both groups but there is obvious difference in number of variants. How can I compare variants of both groups ...
1 vote
2 answers
108 views

How many protein sequences do we usually have for each species?

My question is exactly the one in the title. I add a particular example for more clarity. If I want to study the sequence of protein IkBα, do I find only one sequence or is there a database that ...
0 votes
1 answer
58 views

What do the numbers mean in these RNA-Seq gene/transcript TPM files?

From the link https://gtexportal.org/home/datasets, under V7, I'm trying to do R/Python analyses on the Gene TPM and Transcript TPM files. But in these files (and to open them I had to use Universal ...
4 votes
1 answer
131 views

How can I make this Biopython program (to correct erroneous barcodes) run faster, and is there any alternative method?

This question has also been asked on Biostars I am looking forward to getting a valuable suggestion for a bioinformatic problem. Background: Currently, I am performing a de novo whole genome assembly. ...
-2 votes
1 answer
336 views

How to calculate Allele frequency from vcf file

Organism under investigation is Plasmodium falciparum. How to calculate the allele frequency for each row? I tried with this code: ...
2 votes
1 answer
37 views

Which non-matching DNA bases clash the least?

I am building primers for LAMP which I know will not match all my target sequences perfectly. To some extent, having primers with multiple variants at variable sites (degenerate primers) and longer ...
2 votes
1 answer
73 views

How do I measure the proportion of different bacteria in a sample from a high-throughput sequencer?

[this question is based on a question that was asked on Reddit] I have sequenced some [mostly cell-free] DNA from a sputum sample on a nanopore sequencing machine, and would like to know what is in it ...
1 vote
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Could someone help me understand if all sample within this are control group?

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117872 I'm teaching myself sequence analysis. This is the count data: and then this is, what I believe to be, the coldata: All I want to know is ...
4 votes
2 answers
205 views

Searching motifs in sequence and their frequencies

This is a two part question. I am searching for a motif, and in that search I wanted to also find the total number of sequences in my FASTA file, but the code I wrote is not yielding that please see ...
2 votes
1 answer
116 views

need bam file for pilon

I just ran an assembly on yeast genomes using Flye and I want to polish those assemblies with Pilon but it requires a sorted BAM file. How do I make a BAM file of the resulting assembled.fasta?
1 vote
1 answer
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Maximum likelihood estimation for tree construction

Could someone direct me to a resource (textbook chapter, lecture notes, online video, etc.) that demonstrates, in a mathematically or computationally rigorous way, how to use maximum likelihood ...
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3 answers
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Analysis of 4665 proteins in String database

Background I have a data set of 4665 proteins from Phytophthora cactorum and want to analyze them in the String database as other database does not have Phytophthora cactorum for GO or KEGG analysis. ...
1 vote
1 answer
193 views

What are the columns in bedtools coverage output hist file?

I am using bedtools to caculate the coverage of my targets of my WES data, to later plot. But to plot, I need to know what to plot and what it is I am seeing. I have unsuccefully tried to find what ...
5 votes
2 answers
10k views

Calculating average coverage for .bam files (sequence data)

(Full discolosure that this is my first time working with sequence data, and with the bash scripting.) I need to calculate the average coverage for any .bam file. After some searching I wrote the ...
1 vote
2 answers
89 views

Summing up data effectively in excel

I have some tsRNA count data in excel which I need to add selectively in blocks based on the count ...
1 vote
0 answers
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Generating taxonomic hierarchy by species/genus name

I am attempting to create a reference library of DNA plant barcodes in the ITS2 barcode region for plants from a specific region (Panama). I downloaded all the sequences for plants that resulted in a ...
0 votes
1 answer
915 views

Converting Fastq files to Fasta files on Ubuntu

I am new to bioinformatics and programming. I tried to convert my fastq files to fasta file, but got this. What could be wrong? ...
1 vote
0 answers
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Simple template for calculating Shannon diversity index from FASTQ files with R

I have a bunch of files in FASTQ format and need to calculate the Shannon diversity index from all of them. Is there a simple way to do that with R, some kind of step-by-step recipe? My problem is not ...
1 vote
0 answers
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How to analyze expression of certain group of genes in certain types of cell?

I need to analyze expression of ~ 400 genes with a certain function in the embryonic stem cells. All these genes are combined into one database with RefSeq IDs. What is a recommended workflow to ...