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6 votes

STAR vs Bowtie2

What is the fundamental difference between STAR and Bowtie(2). STAR for mapping spliced (i.e. with introns) short RNA-seq reads against a genome. Bowtie2 for mapping short reads without splicing. ...
user172818's user avatar
  • 6,295
4 votes

How does split reads look like in sam files?

I'm assuming you mean supplementary/chimeric alignment? The SAM Format Specification has a really detailed explanation as well as its Optional Fields Specification. In general though, you will have an ...
helrick's user avatar
  • 94
4 votes

How to align integer (non-DNA/protein) sequences?

The tricky part about your request is the size of the alphabet. If you are happy with alphabets of up to about 250 "characters", then the programs in the FASTA package (github.com/wrpearson/...
Bill Pearson's user avatar
4 votes

Matches, mismatches and indels

Try one of these: GATK: https://gatk.broadinstitute.org/hc/en-us/articles/360036194592-Getting-started-with-GATK4 freebayes: https://bioinformaticsworkbook.org/dataAnalysis/VariantCalling/freebayes-...
story's user avatar
  • 1,568
3 votes

What tool I can use to map short-reads sequences to reference genome and get specific mapped size

If you have a SNP panel then you have the coordinates on the genome. You can use tools such as bedtools slop to expand the coordinates to the desired length and then extract those regions from the ...
asafpr's user avatar
  • 156
3 votes
Accepted

What can be the bias of aligning paired-reads in a single-end mode?

In principle one should simply not align paired-end reads as if they were single end reads, not only because you are not taking advantage of the forward/reverse information contained in the reads, but ...
JRodrigoF's user avatar
  • 705
3 votes

STAR vs Bowtie2

The seeds are clustered together by proximity to a selected set of ‘anchor’ seeds in the 2nd phase of the STAR algorithm, but this •clustering/stitching/scoring process• is not present in Bowtie2. ...
envs_h_gang_5's user avatar
3 votes

Problem with sequence alignment

I don't think that you want an alignment so much as you want to test for the presence of an exact substring (column A) within larger strings (column B). There are simple excel utilities that do this, ...
Maximilian Press's user avatar
3 votes

How to align integer (non-DNA/protein) sequences?

To parse data into pairwise2 so you can follow the SO post here fairly easy by simply converting your output values into a higher base. ...
M__'s user avatar
  • 10.2k
3 votes

BWA-mem and sambamba read group line error

Read groups must start with RG, that is a hardcoded requirement of the SAM format, nothing you can do about that. See https://samtools.github.io/hts-specs/SAMv1.pdf
Clarus Salvus's user avatar
3 votes

MiXCR: only create a single export file for all clonotypes

Currently in MiXCR SERIES 4 you can use --dont-split-files parameter here. Please check our new documentation portal: https://docs.milaboratories.com/mixcr/...
Mark Izraelson's user avatar
3 votes

Read Clustal file in Python

pyMSAviz may help with this problem. pyMSAviz is a Python tool with a convenient CLI/API implementation for visualizing MSA files. For example, you can output MSA figure in PDF format with the ...
moshi's user avatar
  • 31
3 votes

Sanger Sequencing Knitting Error

Your code runs without error on my laptop (macOS 13.2.1; R v4.2.2; Rstudio 2022.07.2), so I have some further questions that might help with troubleshooting (too many to include in a comment): Does ...
jared_mamrot's user avatar
3 votes

Is my reference sequence too small?

That's not the right way to do it. You either have reference or not. If not, you need to assemble one (that problem is called genome assembly). If yes, you map all the reads to the whole reference - ...
Kamil S Jaron's user avatar
2 votes

BLAST(n): No hits found

I came across this thread while searching for a solution to a similar problem I was experiencing. I am inputting markers that are 20 basepairs in length as the query sequence and haven't been getting ...
Brian's user avatar
  • 21
2 votes

multi-sequence alignment of samples with multiple contigs each

in the end, I just loaded the .bam files into artemis and, by inspecting the depth (heat-map), I could check which samples had the genes I was looking for:
BCArg's user avatar
  • 273
2 votes

multi-sequence alignment of samples with multiple contigs each

If you have a reference genome (or are willing to designate one of your de novo assemblies a reference), you may find QUAST helpful. QUAST will perform an alignment of all genomes against the ...
Maximilian Press's user avatar
2 votes

multi-sequence alignment of samples with multiple contigs each

MUMmer4 is a versatile alignment tool for DNA and protein sequences. It supports one reference genome and up to 32 query genomes. MUMmer4 will align every contig in each genome to the reference genome....
Forrest Vigor's user avatar
2 votes

How to chop fasta / bed /peak file genomic segments into smaller fixed or custom genomic intervals

You can run --chop with -x to excise the last piece, adding the --stagger to size the ...
Alex Reynolds's user avatar
2 votes
Accepted

What is the best way to process yeast genomes?

What is your data type? Many assemblers can resolve heterozygosity. PacBio HiFi reads can be used with hifiasm to resolve both haplotypes rather trivially. This is the best case scenario and older ...
Maximilian Press's user avatar
2 votes

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

If you prefer to have a more concise report than a per-base one, bedtools genomecov could be a better choice. Its -bga option allows you to report consecutive bases ...
Siyuan Feng's user avatar
2 votes

Why does the Smith-Waterman algorithm have a complexity of $O(m^2 \times n)$?

I think your source is wrong. You are correct to assume the brunt of its complexity comes from building the $m *n$ matrix. The main differences are in the calculations per cell and the traceback, but ...
Pallie's user avatar
  • 578
2 votes
Accepted

How to identify sequence origin in DNA shuffle reads?

This is the sort of thing that LAST has been specifically designed to work well for: LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially good at finding ...
gringer's user avatar
  • 13k
2 votes

How can I align two novel sequences to a reference genome and build a phylogenetic tree?

Edit: just to point out a tree needs 4 taxa (sequences), so rather than one reference genome, 3 reference genomes. Thus for Blast you might need to produce a database (using 3 reference genomes) ...
M__'s user avatar
  • 10.2k
2 votes
Accepted

Read Clustal file in Python

Ok, figured out a way, not sure its the best one, nedd to install fpdf2 (pip install fpdf2) ...
pippo1980's user avatar
  • 783
2 votes

Read Clustal file in Python

adding, a second answer because the OP request about I need to import the file and then highlight some specific word was making me uneasy. I kept using the Pyfpdf2...
pippo1980's user avatar
  • 783
2 votes
Accepted

How is the "canonical" version (`_entity_poly.pdbx_seq_one_letter_code`) obtained in the PDB?

You can check specification of pdbx_seq_one_letter_code and pdbx_seq_one_letter_code_can. These items are generated from the depositor-provided sequence on the PDB side. I suppose that the software ...
marcin's user avatar
  • 1,176
2 votes

How is the "canonical" version (`_entity_poly.pdbx_seq_one_letter_code`) obtained in the PDB?

So, i was little myopic when reading the PDB description the first few times, but roughly what i was looking for is this: the non-canonical sequence(...
rtviii's user avatar
  • 332
2 votes
Accepted

RNAseq alignment: best practices for aligning to multiple isoforms?

The fact that an alignment is unique or not is relative to the genome, not its annotation. In other words, a read will be considered a multimapper (and ignored by some programs) if it can align to ...
Alexlok's user avatar
  • 277
1 vote

What can be the bias of aligning paired-reads in a single-end mode?

I tried to give me this explanation: with single-end alignment of paired-end reads, losing the directionality of the reads and also the expected fragment length, the R2 no longer maps if it maps the ...
cucalorda's user avatar

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