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6 votes
Accepted

How many false positive duplicates are marked using just the position of first unclipped base?

There's a tool in Picard (full disclaimer: I wrote it...) called CollectIndependentReplicateMetrics which performs the test you are looking for, I think. It measures the percent of duplication that is ...
Yossi Farjoun's user avatar
5 votes
Accepted

Why are Minimap2 alignments different with CIGAR generation flag?

The program's author pointed me to the Minimap2 FAQ: 1. Alignment different with option -a or -c? Without ...
Gawain's user avatar
  • 315
5 votes

Cannot obtain alignment summary after running Bowtie2

Remove the --quiet option, and capture STDERR as well as STDOUT: ...
Timur Shtatland's user avatar
4 votes
Accepted

split fastq file containing a sequence block at different locations

You can try seqkit locate with say start or end of CDS sequence. This will give you a tabulated output with locations of your CDS query in each read. Since you expect that the CDS sequence should be ...
darked89's user avatar
  • 368
3 votes
Accepted

Aligning FASTQs to FASTA reference

Can I expect that after running the command bowtie2 -x ref_index -U seq.fastq.gz -S seq.sam, my seq.sam will only contain the ...
terdon's user avatar
  • 10.2k
3 votes
Accepted

How to know if FASTQ/BAM is from reference genome (FASTA)?

Your post has multiple questions but one of them is not really a question so I'll address everything here: 1. "Some of them could be contaminants, so I'd like to filter them out and get only the ...
Ram RS's user avatar
  • 2,425
2 votes

Cannot obtain alignment summary after running Bowtie2

Get samtools. Then run: samtools stats file.bam and/or samtools flagstat file.bam For example outputs see here.
Maximilian Press's user avatar
2 votes
Accepted

Find protein in DNA sequences with arbitrary encoding and possible frameshifts

If you need to model introns and splicing, then you should use a tool that is designed for that. One of the limitations of blast and its cousins is that they only look at sequence similarity and do ...
terdon's user avatar
  • 10.2k
2 votes
Accepted

How to create a phylogenetic tree from diverse mitochondrial genomes

Your overall approach is cool, given caveats (below) to adapt the method. I can fairly authoritatively say your specific methodological approach will not work regarding its phylogenetic strategy ...
M__'s user avatar
  • 12.6k
2 votes

How to create a phylogenetic tree from diverse mitochondrial genomes

It looks like these are random mitochondrial sequences pulled from NCBI, which is probably why the alignments aren't working well. As a starting point, I recommend you make sure that all the ...
gringer's user avatar
  • 14.4k
2 votes
Accepted

How to convert Foldseek .m8 alignment files to FASTA format?

tl;dr Use an awk script (below) or "one-liner" ...
Ezry's user avatar
  • 36
2 votes
Accepted

BioPython bootstrap is not reliable?

I think this is a bug. It seems to work if you do this, creating an equivalent Alignment object instead of a MultipleSeqAlignment to give the bootstrap step: ...
Jesse's user avatar
  • 947
2 votes
Accepted

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

Its just significant at 2% 0.055 . 65 . 1067 = 0.021 (its actually 0.02 - see note) Where critical probability is 0.05, i.e. 5% There are 20 aa so 1/20 probability of random occurrence. The ...
M__'s user avatar
  • 12.6k
2 votes

How to know if FASTQ/BAM is from reference genome (FASTA)?

In general, this answer wouldn't be more correct than @Ram RS' answer but here is how I would approach: I would start everything from scratch, at the end of the day you will most probably need to ...
haci's user avatar
  • 4,162
2 votes
Accepted

Finding homologous regions in multiple whole genomes

According to show cords the format you are getting contains columns which you can use to obtain BED format with relevant information. You need following columns: <...
darked89's user avatar
  • 368
2 votes

Passing data from the Agilent Trimmer utility to bwa-mem2 via a named pipe

What does this program do in the expected use case, presumably where intermediate output files are generated? From that, can you get any information about how files are updated? For example, are the ...
gringer's user avatar
  • 14.4k
2 votes
Accepted

Where to obtain fastq_illumina_filter

I found this site after Googling fastq_illumina_filter and comparing the file name to that shown in an archived version of your link: https://www.sigenae.org/drap/...
Ram RS's user avatar
  • 2,425
1 vote
Accepted

Creating a Multiple Sequence Alignment From Eggnog Mapper Results

Thanks the qstart and stop are not needed. If you using 'blockwise deletion' in your phylogenetic tree it will ignore the missing sites if this options is selected. The main thing is ...
M__'s user avatar
  • 12.6k
1 vote

How to download the same 18S rRNA gene region for multiple species?

I can suggest two ways to batch-download aligned sequences for the species of interest. Both ways are integral to the Ensembl database and toolsets. But before that, I suggest FBgn0085802 (which is ...
44Pasha's user avatar
  • 21
1 vote

How to download the same 18S rRNA gene region for multiple species?

How do I know which sequence I should use to make an alignment with other species? Use both. For fruit flies there should thousands of 18S sequences. How can I batch download the same region for all ...
M__'s user avatar
  • 12.6k
1 vote

All against all sequence alignment

I wouldn't use Python here. I've looked at using Bio.pairwise2.align. and its has major shortcomings. In this context the problem is establishing homologous ...
M__'s user avatar
  • 12.6k
1 vote

What is the best way to acquire protein isoform sequence alignment?

Here is a manual (or semi-manual, at best) approach. If you need to do this for very many sequences it won't be practical, but if dealing with one or two genes, it might be enough. The idea is to: ...
terdon's user avatar
  • 10.2k
1 vote

align to the whole hg38 genome, then split bam and collect metrics on each bam issue

This can be done, but you have to split the BAMs while keeping the full header (with the dictionary) in place for all the shards. This can be done with gatk PrintReads. One thing to remember is that ...
Yossi Farjoun's user avatar
1 vote

What are the applications of Tries(data structure) of an ordered sequence of strings in bioinformatics?

(Should be a comment not an answer, but I weary of SE comment formatting- feel free to express disapproval in whichever way) When in doubt, google it and look at wikipedia: Tries are used in ...
Maximilian Press's user avatar
1 vote

Sequence Alignment for sequences with the same length

I see ... the application is if two genes had the same number of indels* at different homologous positions within the gene. This happens but equally one gene might have an indel and another gene might ...
M__'s user avatar
  • 12.6k
1 vote

How to create Phylogenetic Trees from fasta files in Python or R?

Within the R/Bioconductor ecosystem you could use the DECIPHER package (https://bioconductor.org/packages/release/bioc/html/DECIPHER.html) to align your sequences ...
Niklas's user avatar
  • 126
1 vote

Pal2nal translation of large multi-fasta files produces a codon translated file where some sequences half length of the average

I had a quick blast of the example sequences and this is the Acacia so ancient vascular plant. It forms a locus within the protein in the first part of the question. This protein is comprises a large ...
M__'s user avatar
  • 12.6k
1 vote

How are BLAST record scores calculated in biopython

The results you'd get are the same as with any other NCBI BLAST+ tools, python does not compute it. Biopython can run a blast query qblast on the internet or ...
3nrique0's user avatar
  • 111

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