seeing a larger file size (with more lines per file) when using 5' merging (vs. without) with cDNA Cupcake

Question

[CaulerpaMan]

Dear Magdoll,

I'm using the Cupcake TOFU scripts in cDNA Cupcake (v. 10), and I find that the number of entries in the output file is actually larger when I allow for 5'-based merging. I would expect to see fewer entries for the 5' merged transcripts, since more merging (vs. less) should decrease the number of overall entries. Could this be a bug? The observation is consistent across file types (GFF, fastq, txt) pertaining to the chained files. As background, I'm chaining together output from 2 SMRT cells, scrubbing the junctions using your 2017 instructions, and using a sequenced genome.

CaulerpaMan

[Kevin Blighe]

'Magdoll' works at Pacific Biosciences (PacBio). You should contact them so that you can get in touch with her. Kevin

Answer 1

[magdoll]

Thank you for the re-direction. For future reference Cupcake can be filed at https://github.com/Magdoll/cDNA_CUpcake/issues and I'll automatically be notified.