Problems with GTF file

[Joe_Hoolachan]

I have recently downloaded a UCSC mm10 reference annotation from the illumina iGenomes site. When downloaded it came as a tar.gz file. I uploaded this tar.gz as GTF on galaxy and encountered no issue with that part. In addition, when used as a GTF for featurecounts from my HISAT2 reads directly there was no issue. However, when I wanted to use it as a GTF for my stringtie straight from HISAT2 an error appeared with this line below. What caused this error?

Error parsing strand ([) from GFF line:
t���P�3<��Fh�@�&P��%��1)�{�e�^u�a����l��=��f_@���m��{݆�ZN��S��Ǚ�9�R��8���0j��D�8ze��X�a��ڏ5��aE�E��y]��s���%jϔ�afW�e.$�s<1���y��y�m��xtz˚Ǹs��:Xy{N � ��oކ�nb�C�A��&���@���B�F��]T�wi��� v�n͡�+� ��8�~Y.���䇃^�GS _ځp� �<1fBE�e 7@������,уut=i!�ig�7��%����a�}D_��љ��U��&�h�Z�g���ݫ�̗A����� [P�۰���p���E�x�|=�6��>H�!����5����p�L R2��$�c���D��܁C

[jennaj]

Hello,

You’ll need to unpack the iGenome archive and just upload the GTF dataset:

RNA-STAR and hg38 GTF reference annotation

For iGenomes , the archive corresponding to the target genome/build needs to be locally downloaded, the tar archive unpacked, and then just the genes.gtf data uploaded to Galaxy (browse the local file, or use FTP). Find all available genome/builds here: https://support.illumina.com/sequencing/sequencing_software/igenome.html

I uploaded this tar.gz as GTF on galaxy and encountered no issue with that part. In addition, when used as a GTF for featurecounts from my HISAT2 reads directly there was no issue.

I would suggest reviewing those results. Suspect the GTF was not actually used correctly.

FAQ: Loading Data

Thanks!

[Joe_Hoolachan]

Hi Jen,

Thank you for the advice. I was just wondering how do you unpack to tar.gz file? as when I tried to convert it to zip and extract the file information it only contained within it another tar file.

Kind regards
Joe

[jennaj]

I was just wondering how do you unpack to tar.gz file?

Try this command:

$ tar -xzf archive.tar.gz

You can google around for more options. Search with the keywords “unpack tar.gz”.

You’ll see some utilities are around that will do the same, it depends where you are working (your OS), but I cannot specifically recommend any of them.