Answers.Body: <p>The most recent annotation of GRCh37 assembly by NCBI RefSeq is here: <a href="https://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/GRCh37.p13_interim_annotation/" rel="nofollow noreferrer">https://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/GRCh37.p13_interim_annotation/</a></p>
  
  <p>You can download the annotation in GFF3 format from that path and use it with featurecounts tool by first converting it to the SAF format using the commands shown below:</p>
  
  <pre><code><span class="math-container">$ zgrep -v '^#' annotation.gff.gz \
      | awk 'BEGIN{FS="\t";OFS="\t"}($</span>3=="exon"){print <span class="math-container">$1,$</span>4,<span class="math-container">$5,$</span>7,<span class="math-container">$9}' \
      | sed -r 's/ID.*GeneID:([0-9]*).*/\1/g' \
      | awk 'BEGIN{FS="\t";OFS="\t"}{print $5,$1,$2,$3,$</span>4}'
      &gt; annotation.saf
  </code></pre>
  
  <p>You should confirm that the chromosome sequence identifiers in the BAM file and the SAF file match. NCBI annotation has identifiers in the accession.version format whereas UCSC uses <code>chr#</code> format and Ensembl uses <code>#</code>. For this, you can use the <code>-A</code> parameter from <code>featureCounts</code>. Assuming that your BAM file uses UCSC-style identifiers, you can generate a 'chromosome name alias file' that can be used with featureCounts as follows: </p>
  
  <pre><code>## get NCBI assembly report for GRCh37
  wget -nv ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.24_GRCh37.p12/GCF_000001405.24_GRCh37.p12_assembly_report.txt
  
  ## generate chr_alias.csv file
  grep -v '^#' GCF_000001405.24_GRCh37.p12_assembly_report.txt \
      | dos2unix \
      | awk 'BEGIN{FS="\t";OFS=","}(<span class="math-container">$10!="na"){print $10,$</span>7}' \
      &gt; chr_alias.csv
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-11T12:06:49.433Z
Answers.Text: I didn't know about "SAF" format. I use gff with FeatureCounts. For the record, according to https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts: "The SAF annotation format has five required columns, including GeneID, Chr, Start, End and Strand. These columns can be in any order".
Answers.UserDisplayName: bli
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-04-10T17:07:57.997Z
Answers.LastActivityDate: 2019-04-10T17:07:57.997Z
Answers.UserDisplayName: vkkodali
Body: <p>I have been given a bunch of .bam files, that come from the alignment on GRCh37d5 of human genome by Star tool. I want to extract raw read counts from these bam files by FEATURECOUNTS tool so I need a GTF. I googled a lot but I did not find GTF for GRCh37d5. I used another GTFs and I obtained weird features. Please one of you help me in finding this specific GTF. I converted a bam to fastq and I used Salmon to quantify gene expression by a transcripome.fasta but rate of mapping was 0.06</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-10T18:30:26.257Z
Comments.Text: It's helpful to know that GRCh37 refers to the **G**enome **R**eference **C**onsortium assembly of the **h**uman genome, version **37** (should be equivalent to hg19 from UCSC). I've never seen "5d" though. Often times GRC will introduce "patch" updates with minor changes that don't change the primary coordinate system—that's what `p13` refers to in kayvee's answer below.
Comments.UserDisplayName: Daniel Standage
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-04-10T18:58:05.973Z
Comments.Text: @DanielStandage Might be of interest to you: https://www.biostars.org/p/328824/#330791
Comments.UserDisplayName: Ram RS
Tags: <rna-seq><phylogenetics><sequence-annotation><gtf>
Title: A GTF annotation for GRCH375d version
ThreadText: # A GTF annotation for GRCH375d version
  
  (Asked by: username_0 on 2019-04-10)
  
  I have been given a bunch of .bam files, that come from the alignment on GRCh37d5 of human genome by Star tool. I want to extract raw read counts from these bam files by FEATURECOUNTS tool so I need a GTF. I googled a lot but I did not find GTF for GRCh37d5. I used another GTFs and I obtained weird features. Please one of you help me in finding this specific GTF. I converted a bam to fastq and I used Salmon to quantify gene expression by a transcripome.fasta but rate of mapping was 0.06
  
  **Tags:** rna-seq, phylogenetics, sequence-annotation, gtf
  
  > **Comments:**
  > **username_1**: It's helpful to know that GRCh37 refers to the **G**enome **R**eference **C**onsortium assembly of the **h**uman genome, version **37** (should be equivalent to hg19 from UCSC). I've never seen "5d" though. Often times GRC will introduce "patch" updates with minor changes that don't change the primary coordinate system—that's what `p13` refers to in kayvee's answer below.  
  > **username_2**: @username_1 Might be of interest to you: https://www.biostars.org/p/328824/#330791  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_3 on 2019-04-10. Score: 2 | Accepted answer
  
  The most recent annotation of GRCh37 assembly by NCBI RefSeq is here: <https://ftp.ncbi.nlm.nih.gov/genomes/Homo_sapiens/GRCh37.p13_interim_annotation/>
  
  You can download the annotation in GFF3 format from that path and use it with featurecounts tool by first converting it to the SAF format using the commands shown below:
  
  ```
  $ zgrep -v '^#' annotation.gff.gz \
      | awk 'BEGIN{FS="\t";OFS="\t"}($3=="exon"){print $1,$4,$5,$7,$9}' \
      | sed -r 's/ID.*GeneID:([0-9]*).*/\1/g' \
      | awk 'BEGIN{FS="\t";OFS="\t"}{print $5,$1,$2,$3,$4}'
      > annotation.saf
  
  ```
  
  You should confirm that the chromosome sequence identifiers in the BAM file and the SAF file match. NCBI annotation has identifiers in the accession.version format whereas UCSC uses `chr#` format and Ensembl uses `#`. For this, you can use the `-A` parameter from `featureCounts`. Assuming that your BAM file uses UCSC-style identifiers, you can generate a 'chromosome name alias file' that can be used with featureCounts as follows:
  
  ```
  ## get NCBI assembly report for GRCh37
  wget -nv ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.24_GRCh37.p12/GCF_000001405.24_GRCh37.p12_assembly_report.txt
  
  ## generate chr_alias.csv file
  grep -v '^#' GCF_000001405.24_GRCh37.p12_assembly_report.txt \
      | dos2unix \
      | awk 'BEGIN{FS="\t";OFS=","}($10!="na"){print $10,$7}' \
      > chr_alias.csv
  
  ```
  
  > **Comments:**
  > **username_4**: I didn't know about "SAF" format. I use gff with FeatureCounts. For the record, according to https://www.rdocumentation.org/packages/Rsubread/versions/1.22.2/topics/featureCounts: "The SAF annotation format has five required columns, including GeneID, Chr, Start, End and Strand. These columns can be in any order".  
  
  ---
  
  