Answers.Body: <p>If you are looking for a genome and its corresponding annotations, you can use the following, it is from <code>nf-core</code> (<a href="https://nf-co.re/docs/usage/reference_genomes" rel="nofollow noreferrer">link to the original doc</a>):</p>
  <pre><code>#!/bin/bash
   
  VERSION=108
  wget -L ftp://ftp.ensembl.org/pub/release-<span class="math-container">$VERSION/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
  wget -L ftp://ftp.ensembl.org/pub/release-$</span>VERSION/gtf/homo_sapiens/Homo_sapiens.GRCh38.$VERSION.gtf.gz
  </code></pre>
  <p>BTW the most up-to-date version as of today is 109.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-23T11:10:35.970Z
Answers.Text: When I use the Ensembl it doesn't work saying `Fatal INPUT FILE error, no valid exon lines in the GTF file:` and then the path to the Ensembl gtf.
Answers.UserDisplayName: Indira
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-24T16:06:14.253Z
Answers.Text: That makes no sense, Ensembl's GTF is the most comprehensive GTF there is.
Answers.UserDisplayName: Ram RS
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-28T23:08:41.147Z
Answers.Text: Thank you @gringer
Answers.UserDisplayName: Indira
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-23T11:05:38.870Z
Answers.LastActivityDate: 2023-08-23T11:05:38.870Z
Answers.UserDisplayName: haci
Answers.Body: <p>I've had success in the past generating STAR indexes using the Gencode GTF files available from here:</p>
  <p><a href="https://www.gencodegenes.org/human/" rel="nofollow noreferrer">https://www.gencodegenes.org/human/</a></p>
  <ul>
  <li>Comprehensive gene annotation (ALL regions)</li>
  <li>Genome sequence (ALL)</li>
  </ul>
  <p>If you make sure that you're getting both the genome and the GTF files from the same source, it's more likely that they will work well together.</p>
  <p>Note that the ALL annotation includes assembly patches and alternate haplotypes. The alternate haplotypes mean that population variation is captured, which usually increases the alignment rate of reads.</p>
  <p>Unfortunately, most bioinformatics workflows don't properly handle alternate assemblies. As one example, reads aligning to those areas may end up classified as mapping to multiple genomic locations, even though they actually aren't. So it's a tradeoff of a more accurate alignment vs more hassle dealing with those alignments downstream.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2023-08-24T06:15:12.023Z
Answers.LastActivityDate: 2023-08-26T10:10:17.280Z
Answers.LastEditDate: 2023-08-26T10:10:17.280Z
Answers.UserDisplayName: gringer
Body: <p>To make a STAR reference genome used for alignment you need a genome fasta (the resources fasta provided by the Broad Institute in my case) and a GTF fasta. I tried to use the Ensembl human genome fasta fro hg38 but that does not work. I have looked in the <a href="https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/" rel="nofollow noreferrer">GATK resources package</a> but there is no <code>.gtf</code> file there. I really don't know what to do in this case? Is there anyone who can provide some guidance as to what <code>.gtf</code> file I should use?</p>
  
Tags: <star>
Title: GTF To Use With Broad Institute Fasta In STAR
ThreadText: # GTF To Use With Broad Institute Fasta In STAR
  
  (Asked by: username_0 on 2023-08-23)
  
  To make a STAR reference genome used for alignment you need a genome fasta (the resources fasta provided by the Broad Institute in my case) and a GTF fasta. I tried to use the Ensembl human genome fasta fro hg38 but that does not work. I have looked in the [GATK resources package](https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0/) but there is no `.gtf` file there. I really don't know what to do in this case? Is there anyone who can provide some guidance as to what `.gtf` file I should use?
  
  **Tags:** star
  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_1 on 2023-08-23. Score: 1 | Accepted answer
  
  If you are looking for a genome and its corresponding annotations, you can use the following, it is from `nf-core` ([link to the original doc](https://nf-co.re/docs/usage/reference_genomes)):
  
  ```
  #!/bin/bash
   
  VERSION=108
  wget -L ftp://ftp.ensembl.org/pub/release-$VERSION/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
  wget -L ftp://ftp.ensembl.org/pub/release-$VERSION/gtf/homo_sapiens/Homo_sapiens.GRCh38.$VERSION.gtf.gz
  
  ```
  
  BTW the most up-to-date version as of today is 109.
  
  > **Comments:**
  > **username_0**: When I use the Ensembl it doesn't work saying `Fatal INPUT FILE error, no valid exon lines in the GTF file:` and then the path to the Ensembl gtf.  
  > **username_2**: That makes no sense, Ensembl's GTF is the most comprehensive GTF there is.  
  > **username_0**: Thank you @username_3  
  
  ---
  
  ### Answer by username_3 on 2023-08-24. Score: 1
  
  I've had success in the past generating STAR indexes using the Gencode GTF files available from here:
  
  <https://www.gencodegenes.org/human/>
  
  * Comprehensive gene annotation (ALL regions)
  * Genome sequence (ALL)
  
  If you make sure that you're getting both the genome and the GTF files from the same source, it's more likely that they will work well together.
  
  Note that the ALL annotation includes assembly patches and alternate haplotypes. The alternate haplotypes mean that population variation is captured, which usually increases the alignment rate of reads.
  
  Unfortunately, most bioinformatics workflows don't properly handle alternate assemblies. As one example, reads aligning to those areas may end up classified as mapping to multiple genomic locations, even though they actually aren't. So it's a tradeoff of a more accurate alignment vs more hassle dealing with those alignments downstream.
  
  
  ---
  
  