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

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

rna-seq
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updated by magdoll • magdoll • written by CaulerpaMan • CaulerpaMan

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

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written by Kevin Blighe Kevin Blighe

1 answer

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.

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written by magdoll • magdoll

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