Hey guys,
I am analyzing my RNA-seq data on Galaxy platform using Tophat-Cufflink-Cuffdiff pipeline. I aligned my reads with hg38 but for cuffdiff I need a well annotated, working hg38 gtf file. I already tried a gtf file on hg38 from UCSC but it didn't work.
Is there someone done such analysis on hg38 gtf file? If so, please provide me the download link for the same.
Thanks
Have a look here: ftp://ftp.ensembl.org/pub/release-84/gtf/homo_sapiens (and if that doesn't work, like the UCSC file, specify what goes wrong so we can troubleshoot)
Did it worked for you in Cuffdiff analysis? I am sure that I used this file (the link you gave) for Cuffdiff and it didn't show up any differential expression status.
Did it worked for you in Cuffdiff analysis? I am sure that I used this file (the link you gave) for Cuffdiff and it didn't show up any differential expression status.
Please use the comment feature rather than a separate answer when replying. I haven't used cuffdiff/galaxy. From where did you get the hg38 reference genome or index files?
I have used Homo_sapiens.GRCh38.cdna.all.fa file as a reference genome and in Tophat2, it aligned well enough. But I faced the problem with gtf file.
Pretty sure you should in this workflow align to genome, not to transcriptome. Explains why coordinates of gtf don't match anything.
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