Skip to main content
24 votes
Accepted

Convert a BAM file from one reference to another?

You're the second person I have ever seen using NCBI "chromosome names" (they're more like supercontig IDs). Normally I would point you to a resource providing mappings between chromosome names, but ...
Devon Ryan's user avatar
  • 19.7k
11 votes

Downloading a reference Genome for Bowtie2

It’s a matter of preference I guess but I recommend the Ensembl builds. Decide whether you want the toplevel or primary assembly, and whether you want soft-masked, repeat-masked or unmasked files. The ...
Konrad Rudolph's user avatar
9 votes
Accepted

Downloading a reference Genome for Bowtie2

tl;dr: Just use the either the downloads on the Bowtie2 homepage or the Illumina iGenomes. Or just uncompress and concatenate the FASTA files found on UCSC goldenpath and then build the index. A bit ...
Manuel's user avatar
  • 588
8 votes
Accepted

Why do these NCBI representative genomes for ape species have no Y chromosome?

tl;dr: technical difficulties, or sex For the gorilla, that genome is from a female gorilla (Kamilah the gorilla) so she doesn't have a Y chromosome. For the chimp link, there is a visualization of ...
Maximilian Press's user avatar
7 votes

How to manipulate a reference FASTA or bam to include variants from a VCF?

GATK has a solution that might work for you: FastaAlternateReferenceMaker, which : "Given a variant callset, this tool replaces the reference bases at variation sites with the bases supplied in the ...
Greg's user avatar
  • 831
7 votes
Accepted

What are all the reference files produced by bwa index, and are these dependent upon whether the reference is zipped?

You'll get the exact same index (the amb, ann, bwt, pac ...
Devon Ryan's user avatar
  • 19.7k
6 votes

What is the standard way to work with a diploid reference genome? Complementary strands?

At the moment, the standard reference genomes (e.g. hg19, hg38) are haploid genomes. We know that the human genome is diploid. Naturally, the latter would be the respectively correct representation of ...
winni2k's user avatar
  • 2,286
5 votes
Accepted

Bacterial genome annotation of a clinical isolate strain?

For a quick (but reliable) analysis, I'd recommend using Kallisto or Salmon to quantify isoform read counts using the transcriptome of the lab strain. If you have a concern about transcripts that are ...
gringer's user avatar
  • 14.6k
5 votes
Accepted

What is the standard way to work with a diploid reference genome? Complementary strands?

For calling small variants, the standard way is to simply call diploid genotypes. You can already do a variety of research with unphased genotypes. You may further phase genotypes with imputation, ...
user172818's user avatar
  • 6,575
5 votes

Which reference to use for read mapping for popular model organisms

I will answer one of the points – E.coli. TL;DR Bacteria, and in particular E.coli, are highly variable and there is usually no single best assembly. Large scale WGS studies should come with multiple ...
Karel Břinda's user avatar
4 votes

Convert a BAM file from one reference to another?

The "right" solution would be realignment, but that's expensive and most of us would not go that route. My preferred solution would be to convert the bed file, as opposed to the bam. Here's why: 1) ...
chrisamiller's user avatar
4 votes
Accepted

How to manipulate a reference FASTA or bam to include variants from a VCF?

You could convert VCF to BED via vcf2bed --snvs, vcf2bed --insertions, and ...
Alex Reynolds's user avatar
4 votes

What process and input data is required for a cellranger reference transcriptome?

Your problem is caused by using the transcriptome fasta file rather than the genome fasta file. You've already given it transcriptome information with ...
Devon Ryan's user avatar
  • 19.7k
4 votes
Accepted

How to find novel transcripts using GFFcompare?

The output of gffcompare includes several files per run (just like cuffcompare). Example for a run: ...
aechchiki's user avatar
  • 2,696
4 votes

Are there open-sourced graph-based variant callers?

Yes, there are. There are some suggestions in the comments (VG, WhatsHap, GraphAligner, Minigraph). However, to be clear, the current default variant calling algorithm used in the GATK (the haplotype ...
winni2k's user avatar
  • 2,286
3 votes
Accepted

How to get results from Homo.sapiens package in bioconductor for a specific reference

I couldn't find how is this package build, my guess is that is as in the example of the OrganismDBI package. See that vignette section to build your own data package with the genome you want. The ...
llrs's user avatar
  • 4,713
3 votes
Accepted

How can I subset a reference based on only the first chromosome?

It sounds like you want samtools faidx foo.fa followed by samtools faidx foo.fa chr1 > your_subset_file.fa (or whatever the ...
Devon Ryan's user avatar
  • 19.7k
3 votes

What is the standard way to work with a diploid reference genome? Complementary strands?

To add to all the other great answers, I would mention that the question is somewhat misleading. If the reference genome is for a single individual, then it should be diploid. However, it's a ...
burger's user avatar
  • 2,199
3 votes

How to manipulate a reference FASTA or bam to include variants from a VCF?

There's a vcf2fq sub-program that was written as part of vcfutils to convert a VCF file into a fastq file given a reference sequence. Unfortunately this doesn't ...
gringer's user avatar
  • 14.6k
3 votes
Accepted

Is it possible to do alignment within Python? Check variants against reference?

As others have said, doing whole-genome (or even whole-chromosome) alignments is the wrong solution. Simply track where you're creating SNVs. If you wrote your SNV locations to a sorted BED file you ...
Devon Ryan's user avatar
  • 19.7k
3 votes
Accepted

Given a Genomic Ranges of SNPs, how to inject these SNPs in genome via BSGenome?

This seems relatively complicated given the structure of a BSGenome object. The creator of the package answered this question previously on the Bioconductor support forums: https://support....
story's user avatar
  • 1,603
3 votes

Number of reference sequences in a SAM file

There are multiple ways. Here are two: samtools idxstats ‹bamfile› samtools view -H ‹bamfile› | grep '^@SQ' Both commands give ...
Konrad Rudolph's user avatar
3 votes
Accepted

At what stage of a transcriptome assembly is it better to perform read contaminant filter?

First, to answer your question about mapping to a low-quality reference: 1. Mapping For mapping, low genome contiguity (low N50) doesn't really matter. You will be using a spliced aligner and short ...
conchoecia's user avatar
  • 3,181
3 votes

BWA: Detecting Variation between Reference Genome and Short-Read Sequences

I haven't done any whole-genome STR analysis from NGS data myself, but are aware of others that have used lobSTR for this. There's also a recent paper [here] that compares a few different STR analysis ...
gringer's user avatar
  • 14.6k
3 votes

file path of BiocManager:install()

First, I would try again to download via the bioconductor command. If your internet is intermittent it may just take a few tries. If that doesn't work, I would then strongly recommend using ...
Maximilian Press's user avatar
3 votes
Accepted

How to subset an SRA file for a single chromosome?

After dumping out the reads using fasterq-dump, you'll need to align them first and then extract those that map to your region of interest. I think minimap2 is an ...
Steve's user avatar
  • 3,118
3 votes
Accepted

Which human reference genome version does VARAdb use?

They are using hg19. I found this by simply going to "Browse" then copying taking the first rsID in the list (rs1891805) and comparing the chromosomal position they give in VARAdb to what I ...
terdon's user avatar
  • 10.3k
2 votes

What is the standard way to work with a diploid reference genome? Complementary strands?

There are some assemblers that produce assembly graphs that attempt to describe all the possible haploid paths within a set of reads. Such an assembly attempts to capture all the diploid variation (...
gringer's user avatar
  • 14.6k
2 votes

Can a customized GRCh38 .gtf file be used with any of the GRCh38 released patches?

You can see the exact assembly by looking in the README file in Ensembl's genome download page. ftp://ftp.ensembl.org/pub/release-89/fasta/homo_sapiens/dna/README As you can see the current assembly ...
tweirick's user avatar
  • 171
2 votes

Which reference to use for read mapping for popular model organisms

If the programs you are using allow for it, take the most recent available genome, as it will be most likely to have the fewest errors. Many of the well-known model organisms have an official release ...
gringer's user avatar
  • 14.6k

Only top scored, non community-wiki answers of a minimum length are eligible