arefeen
commented
4 years ago Hi Alan,
Thanks a lot for using TAPAS. I have collected the annotation file (refFlat format) from UCSC genome browser. But, I think UCSC has a tool to convert a GTF file to a refFlat file. Please check whether the tool converts correctly (by comparing the format of the tool generated refFlat with a UCSC refFlat). Or you can construct a script that produce a refFlat file from any kind of file (keeping proper format). My advice is to be as consistent as possible (if you use version x in downstream then please use the same version in upstream). You can also read the TAPAS paper in bioinformatics.
Thanks, Ashraful
On Tue, Dec 10, 2019, 3:23 PM AlanMonziani notifications@github.com wrote:
Hello, I am currently running TAPAS starting from reads aligned on the on the GRCh38_snp_tran_genome, corresponding to UCSC hg38. First I tried by using the annotation file you provide, but then I realized it was made starting from GRCh37 release, thus not being suitable (in fact, no APA were detected). What are the steps required to make the correct annotation file? Would be a GTF file a good starting point? Moreover, do you think the actual release of the GRCh38 used for upstream alignments would affect downstream results/matching with annotation files (like GRCh38 release 92 vs 96 vs 98 and so on)?
Many thanks!
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Hello, I am currently running TAPAS starting from reads aligned on the on the GRCh38_snp_tran_genome, corresponding to UCSC hg38. First I tried by using the annotation file you provide, but then I realized it was made starting from GRCh37 release, thus not being suitable (in fact, no APA were detected). What are the steps required to make the correct annotation file? Would be a GTF file a good starting point? Moreover, do you think the actual release of the GRCh38 used for upstream alignments would affect downstream results/matching with annotation files (like GRCh38 release 92 vs 96 vs 98 and so on)?
Many thanks!