geneset.gtf location

[wwinnerhoo]

Hi,

I am stuck in the "--gene-tag=XT" parameter for our single-cell data based on CEL-seq2 using "umi_tools count" tool. I tried the test dataset named "hgmm_100_fastqs.tar", however, the "geneset.gtf" file applied in featureCounts command was lost. Could you please tell me where I can download this file? Alternatively, how did you get the "hg38_noalt_junc85_99.dir" folder? I wish to reproduce your results as detailed as possible.

THanks for your help!

Best, Hoo

[IanSudbery]

The geneset we used in this example was based on: https://ftp.ensembl.org/pub/release-85/gtf/homo_sapiens/Homo_sapiens.GRCh38.85.gtf.gz

except that the chromosomes have been renamed to their UCSC/Gencode equivalents.

For all intents and purposes which should be functionally equivalent to GENCODE version 24.

[wwinnerhoo]

Hi IanSudbery,

Thanks for your quick reply!! Could you also give me the reference genome in fasta format (or address) to build the index of the home genome?

Best, Hoo

[IanSudbery]

http://hgdownload.cse.ucsc.edu/goldenPath/hg38/bigZips/analysisSet/hg38.analysisSet.fa.gz with any _alt and _hap contigs removed.

[wwinnerhoo]

Great! 🥳