Delaney Sullivan
Delaney Sullivan
Yes, the GTF file needs to have transcript records. Only having exon records will not work. As for fixing kallisto's issue to better handle GTF input (or better documentation of...
That's fair, and I do hope to work on an improved genomebam-like feature in the near future, because I actually do need visual tracks for some of my projects (e.g....
Long-winded answer: Correct, pseudobam was very hard to maintain, especially within the logic of the new de bruijn graph structure that was implemented in the latest release. As such, it...
Ah yes, the equivalence class is basically a collection of transcripts. So if an equivalence class consists of transcripts A, B, and C — it means that the k-mers in...
No, you don’t have to include the patches
Can you check if your Homo_sapiens.GRCh38.cdna.all.fa file actually contains anything?
You should be using kallisto bus --aa for pseudoalignment. Recommend that you use the kb-python program for these purposes.
bustools count, by default, collapses the UMIs. If you want to ignore the UMIs when counting reads, use bustools count with the --cm option.
That can definitely happen. Let's say you have 3 reads with the exact same UMI. - Read 1 maps to genes A, B - Read 2 maps to gene A,...
UMIs are always collapsed at gene-level regardless. The final "collapsed" UMI should belong to a single gene (and the equivalence class would contain multiple transcripts associated with that gene). For...