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 ...
- 19.6k
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 ...
- 4,845
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 ...
- 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 ...
- 3,804
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 ...
- 841
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 ...
- 19.6k
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 ...
- 2,236
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, ...
- 6,485
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 ...
- 1,899
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) ...
- 530
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 ...
- 3,125
4
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 ...
- 13.8k
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 ...
- 19.6k
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:
...
- 2,676
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 ...
- 2,236
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 ...
- 4,693
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 ...
- 19.6k
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 ...
- 2,169
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 ...
- 13.8k
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 ...
- 19.6k
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....
- 1,573
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 ...
- 4,845
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 ...
- 3,141
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 ...
- 13.8k
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 ...
- 3,804
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 ...
- 3,059
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 ...
- 9,662
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 (...
- 13.8k
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 ...
- 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 ...
- 13.8k
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