23 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 ...
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  • 19.2k
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 ...
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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 ...
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  • 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 ...
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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 ...
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  • 841
6 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 ...
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  • 19.2k
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 ...
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  • 2,086
5 votes
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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, ...
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  • 5,764
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 ...
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4 votes
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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 ...
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  • 11.8k
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) ...
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4 votes
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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 ...
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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 ...
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  • 19.2k
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: ...
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  • 2,646
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 ...
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  • 2,086
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 ...
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  • 11.8k
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 ...
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  • 19.2k
3 votes
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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....
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  • 1,498
3 votes
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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 ...
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  • 4,622
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 ...
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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 ...
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  • 3,081
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 ...
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  • 11.8k
2 votes
Accepted

Does the galGal5 chicken assembly have a chromosome 29?

The current ensembl entry doesn't have a 29 either. The archived ensembl assembly lacks 29 30, and 31 and 33 and LGE64. The chromosomes after 30 are tiny, so they might not be visible in a ...
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  • 1,672
2 votes

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

If you store the positions of your random SNPs in a sort-bed sorted BED file, you can filter with BEDOPS bedmap: ...
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2 votes
Accepted

Two variants associated with same chromosomal position in genotype data for one individual

First of all, take these data with a very large pinch of salt. This sort of targeted analysis is not designed to produce high quality genetic data but, to give an idea of a sample's ancestry. Given a ...
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  • 8,151
2 votes

Two variants associated with same chromosomal position in genotype data for one individual

It's pretty common for SNPs and indels that map to the same position in the genome to be assigned different rsIDs, particularly when the indel spans multiple base pairs in the reference. You can get ...
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  • 1,806
2 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 ...
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  • 19.2k
2 votes

population admixture

Disclaimer, I am not an expert on admixture, answer is provided without any warranty. It depends what you want to figure out. Why do you want to categorize the ancestry of the individual? If you ...
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  • 5,327
2 votes
Accepted

Java error when launching Pilon

Like gringer already commented, the cause of your error is nicely given by the java program. Your default max heap settings are ...
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  • 3,551
2 votes

Creating a new reference genome B by changing genome A with mismatches from BAM file without long reads

You should be able to use something like Pilon to convert from one genome to another, assuming the changes are all fairly small local changes (but that's almost never the case). I find your ...
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  • 11.8k

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