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<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal">I needed the human ERBB2 gene fasta formatted sequence and the corresponding GTF, which I downloaded from the Ensembl site.<o:p></o:p></p>
<p class="MsoNormal">Then I added these to the mouse ref fasta and gtf respectively and tried to build the index.<o:p></o:p></p>
<p class="MsoNormal">This is needed because I have a mouse tumor sequencing data that I am analyzing for a whole transcriptome RNAseq study and the human ERBB2 has been knocked-in.<o:p></o:p></p>
<p class="MsoNormal">I am getting the following error in the GTF format:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">cellranger mkgtf \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">> Mus_musculus.GRCm38.84.gtf \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">> Mus_musculus.GRCm38.84.filtered.gtf \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">> --attribute=gene_biotype:protein_coding \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">> --attribute=gene_biotype:lincRNA \<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">> --attribute=gene_biotype:antisense<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">/GenomicPrimaryData/installs/10X/cellranger-2.2.0/cellranger-cs/2.2.0/bin<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">cellranger mkgtf (2.2.0)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">Copyright (c) 2018 10x Genomics, Inc. All rights reserved.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">-------------------------------------------------------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">Writing new genes GTF file (may take 10 minutes for a 1GB input GTF file)...<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">Property 'transcript_id' not found in GTF line 1591734: 17 Ensembl exon 39687834 39688057 . - . Name=ENSE00003599710;Parent=ENST00000579146<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:8.0pt;font-family:"Courier New"">Please fix your GTF and start again.<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The line that is causing the problem is:<o:p></o:p></p>
<p class="MsoNormal">17 Ensembl <span style="background:yellow;mso-highlight:yellow">
exon</span> 39687834 39688057 . - . Name=ENSE00003599710;Parent=ENST00000579146<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Can you please help with troubleshooting this problem.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">- Pankaj<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">-----------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Pankaj Agarwal, M.S<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Bioinformatician<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Data Analyst<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Applied Therapeutics<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Div. of Surgical Sciences<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Dept. of Surgery<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">Duke University<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">M: 919-244-6389<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif"">O: 919-681-2251<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:7.0pt;font-family:"Verdana","sans-serif""><a href="mailto:p.agarwal@duke.edu"><span style="color:blue">p.agarwal@duke.edu</span></a><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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