In our #RNAseq & #scRNAseq work we use @ensembl's databases. Two months ago @sinabooeshaghi noticed some inconsistencies between @ensembl's cDNA fasta and GTF files and investigated with @lioscro. Now @LambdaMoses has written up an in-depth analysis:https://fromsystosys.netlify.com/2020/01/31/comparing-ensembl-gtf-and-cdna/ …
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I’ve always wondered how disadvantageous reinventing the wheel actually is given stuff like this. One of the first pieces of workhorse code I wrote in grad school was an annot. parser to generate CDSes from a genome, but clearly using shared tools is in theory much better...
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Actually once I have also tried to brute force extract CDSes and splice the exons together, until I discovered extractTranscriptSeqs from the Bioconductor package GenomicFeatures
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