Answers.Body: <p>I stumbled across this issue after getting the same warning message from <code>liftOver</code>. By using the <code>-out</code> option of <code>lgHgGene</code>, the <code>database</code> parameter is ignored but must still be provided. The <code>table</code> parameter should be the second column from your GTF file. Note that you must also specify the <code>-gtf</code> option (otherwise it expects GFF format). In my case, the GTF file looks like:</p>
  
  <pre><code>chr1    mm10_knownGene  exon    3073253 3074322 0.000000        +       .       gene_id "ENSMUST00000193812.1"; transcript_id "ENSMUST00000193812.1";
  chr1    mm10_knownGene  exon    3102016 3102125 0.000000        +       .       gene_id "ENSMUST00000082908.1"; transcript_id "ENSMUST00000082908.1";
  chr1    mm10_knownGene  exon    3206523 3207317 0.000000        -       .       gene_id "ENSMUST00000159265.1"; transcript_id "ENSMUST00000159265.1";
  chr1    mm10_knownGene  exon    3213439 3215632 0.000000        -       .       gene_id "ENSMUST00000159265.1"; transcript_id "ENSMUST00000159265.1";
  chr1    mm10_knownGene  exon    3205901 3207317 0.000000        -       .       gene_id "ENSMUST00000162897.1"; transcript_id "ENSMUST00000162897.1";
  chr1    mm10_knownGene  exon    3213609 3216344 0.000000        -       .       gene_id "ENSMUST00000162897.1"; transcript_id "ENSMUST00000162897.1";
  ...
  </code></pre>
  
  <p>By default, <code>ldHgGene</code> outputs a leading 'bin' column which won't work with <code>liftOver</code>; this can be avoided with the <code>-nobin</code> option. So my command was:</p>
  
  <pre><code>ldHgGene -gtf -nobin -out=mm10.GENCODE_VM20.gp ignored mm10_knownGene mm10.GENCODE_VM20.gtf
  </code></pre>
  
  <p>The resulting genePred output can be fed directly into <code>liftOver -genePred</code>:</p>
  
  <pre><code>ENSMUST00000193812.1    chr1    +       3073252 3074322 3074322 3074322 1       3073252,        3074322,
  ENSMUST00000082908.1    chr1    +       3102015 3102125 3102125 3102125 1       3102015,        3102125,
  ENSMUST00000162897.1    chr1    -       3205900 3216344 3216344 3216344 2       3205900,3213608,        3207317,3216344,
  ENSMUST00000159265.1    chr1    -       3206522 3215632 3215632 3215632 2       3206522,3213438,        3207317,3215632,
  </code></pre>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-06-13T18:26:31.503Z
Answers.LastActivityDate: 2019-06-13T18:26:31.503Z
Answers.UserDisplayName: knowah
Body: <p>I want to lift over the annotation from <em>E. coli</em> release 29 to <em>E. coli</em> release 42. I have followed the steps for an annotation liftover mentioned <a href="http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver" rel="nofollow noreferrer">here</a>. I got the chain file for the final step and ran:</p>
  
  <p><code>liftOver -gff Escherichia_coli.GCA_000967155.1.gtf Chromosome.chain conversions.gtf unmapped.gtf</code></p>
  
  <p>However, I get the following warning:</p>
  
  <pre><code>WARNING: -gff is not recommended.
  Use 'ldHgGene -out=&lt;file.gp&gt;' and then 'liftOver -genePred &lt;file.gp&gt;'
  </code></pre>
  
  <p>I would like to heed the warning. However, I don't know how to use the <code>ldHgGene</code> tool. Here is its help page:</p>
  
  <pre><code>ldHgGene - load database with gene predictions from a gff file.
  usage:
       ldHgGene database table file(s).gff
  options:
       -bin         Add bin column (now the default)
       -nobin       don't add binning (you probably don't want this)
       -exon=type   Sets type field for exons to specific value
       -oldTable    Don't overwrite what's already in table
       -noncoding   Forces whole prediction to be UTR
       -gtf         input is GTF, stop codon is not in CDS
       -predTab     input is already in genePredTab format
       -requireCDS  discard genes that don't have CDS annotation
       -out=gpfile  write output, in genePred format, instead of loading
                    table. Database is ignored.
       -genePredExt create a extended genePred, including frame
                    information and gene name
       -impliedStopAfterCds - implied stop codon in GFF/GTF after CDS
  </code></pre>
  
  <p>From what I understand, I am trying to give the liftOver tool the annotation in <a href="http://genome.ucsc.edu/FAQ/FAQformat.html#format9" rel="nofollow noreferrer">GenePred format</a> instead of GTF format. So I need to convert the GTF format into a GenePred format and that's what the ldHgGene tool is for. So the command should be something like:</p>
  
  <pre><code>ldHgGene Escherichia_coli.GCA_000967155.1.gtf -out=Escherichia_coli.GCA_000967155.1.gp
  </code></pre>
  
  <p>but this returns nothing. The <code>-out</code> option does mean that the <code>database</code> parameter is not needed but the tool still seems to need the parameter <code>table</code>. </p>
  
  <p>What is the <code>table</code> parameter?</p>
  
Tags: <format-conversion><sequence-annotation><ucsc><liftover>
Title: What is the `table` parameter in the UCSU ldHgGene tool?
ThreadText: # What is the `table` parameter in the UCSU ldHgGene tool?
  
  (Asked by: username_0 on 2019-04-29)
  
  I want to lift over the annotation from *E. coli* release 29 to *E. coli* release 42. I have followed the steps for an annotation liftover mentioned [here](http://genomewiki.ucsc.edu/index.php/Minimal_Steps_For_LiftOver). I got the chain file for the final step and ran:
  
  `liftOver -gff Escherichia_coli.GCA_000967155.1.gtf Chromosome.chain conversions.gtf unmapped.gtf`
  
  However, I get the following warning:
  
  ```
  WARNING: -gff is not recommended.
  Use 'ldHgGene -out=<file.gp>' and then 'liftOver -genePred <file.gp>'
  
  ```
  
  I would like to heed the warning. However, I don't know how to use the `ldHgGene` tool. Here is its help page:
  
  ```
  ldHgGene - load database with gene predictions from a gff file.
  usage:
       ldHgGene database table file(s).gff
  options:
       -bin         Add bin column (now the default)
       -nobin       don't add binning (you probably don't want this)
       -exon=type   Sets type field for exons to specific value
       -oldTable    Don't overwrite what's already in table
       -noncoding   Forces whole prediction to be UTR
       -gtf         input is GTF, stop codon is not in CDS
       -predTab     input is already in genePredTab format
       -requireCDS  discard genes that don't have CDS annotation
       -out=gpfile  write output, in genePred format, instead of loading
                    table. Database is ignored.
       -genePredExt create a extended genePred, including frame
                    information and gene name
       -impliedStopAfterCds - implied stop codon in GFF/GTF after CDS
  
  ```
  
  From what I understand, I am trying to give the liftOver tool the annotation in [GenePred format](http://genome.ucsc.edu/FAQ/FAQformat.html#format9) instead of GTF format. So I need to convert the GTF format into a GenePred format and that's what the ldHgGene tool is for. So the command should be something like:
  
  ```
  ldHgGene Escherichia_coli.GCA_000967155.1.gtf -out=Escherichia_coli.GCA_000967155.1.gp
  
  ```
  
  but this returns nothing. The `-out` option does mean that the `database` parameter is not needed but the tool still seems to need the parameter `table`.
  
  What is the `table` parameter?
  
  **Tags:** format-conversion, sequence-annotation, ucsc, liftover
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-06-13. Score: 3 | Accepted answer
  
  I stumbled across this issue after getting the same warning message from `liftOver`. By using the `-out` option of `lgHgGene`, the `database` parameter is ignored but must still be provided. The `table` parameter should be the second column from your GTF file. Note that you must also specify the `-gtf` option (otherwise it expects GFF format). In my case, the GTF file looks like:
  
  ```
  chr1    mm10_knownGene  exon    3073253 3074322 0.000000        +       .       gene_id "ENSMUST00000193812.1"; transcript_id "ENSMUST00000193812.1";
  chr1    mm10_knownGene  exon    3102016 3102125 0.000000        +       .       gene_id "ENSMUST00000082908.1"; transcript_id "ENSMUST00000082908.1";
  chr1    mm10_knownGene  exon    3206523 3207317 0.000000        -       .       gene_id "ENSMUST00000159265.1"; transcript_id "ENSMUST00000159265.1";
  chr1    mm10_knownGene  exon    3213439 3215632 0.000000        -       .       gene_id "ENSMUST00000159265.1"; transcript_id "ENSMUST00000159265.1";
  chr1    mm10_knownGene  exon    3205901 3207317 0.000000        -       .       gene_id "ENSMUST00000162897.1"; transcript_id "ENSMUST00000162897.1";
  chr1    mm10_knownGene  exon    3213609 3216344 0.000000        -       .       gene_id "ENSMUST00000162897.1"; transcript_id "ENSMUST00000162897.1";
  ...
  
  ```
  
  By default, `ldHgGene` outputs a leading 'bin' column which won't work with `liftOver`; this can be avoided with the `-nobin` option. So my command was:
  
  ```
  ldHgGene -gtf -nobin -out=mm10.GENCODE_VM20.gp ignored mm10_knownGene mm10.GENCODE_VM20.gtf
  
  ```
  
  The resulting genePred output can be fed directly into `liftOver -genePred`:
  
  ```
  ENSMUST00000193812.1    chr1    +       3073252 3074322 3074322 3074322 1       3073252,        3074322,
  ENSMUST00000082908.1    chr1    +       3102015 3102125 3102125 3102125 1       3102015,        3102125,
  ENSMUST00000162897.1    chr1    -       3205900 3216344 3216344 3216344 2       3205900,3213608,        3207317,3216344,
  ENSMUST00000159265.1    chr1    -       3206522 3215632 3215632 3215632 2       3206522,3213438,        3207317,3215632,
  
  ```
  
  
  ---
  
  