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Novi razgovor
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Bottom line: If you want paired files use
@GencodeGenes via http://gencodegenes.org (where The "Comprehensive gene annotation" GTF and the "Transcript sequences" fasta file is a perfect pair)Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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I just came across this same issue a few months ago when developing kb. It's alarming that there is no clear documentation explaining the discrepancy.
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Which is why I believe many tools choose to split the genome manually using a GTF.
- Još 3 druga odgovora
Novi razgovor -
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The offical reply I got when asking: - GTF files found here are equivalent to the
@GencodeGenes set - The FASTA only contain cDNA sequences corresponding to Ensembl gene predictions. - Furthermore, we have also imported transcripts from RefSeqPrikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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Or use whatever GTF file you want + gffread (distributed with Stringtie, Cufflinks or available here: https://github.com/gpertea/gffread )
Prikaži ovu nitHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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This Google Colab tutorial shows how to generate a matching genome-transcriptome pair using kallisto and bustools (via kb): https://colab.research.google.com/github/pachterlab/kallistobustools/blob/master/notebooks/kb_transcriptome_index.ipynb … cc
@sinabooeshaghi@lioscroHvala. Twitter će to iskoristiti za poboljšanje vaše vremenske crte. PoništiPoništi
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