cDNA_Cupcake
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Magdoll
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
I've encountered and fixed a couple of bugs with [make_file_for_subsampling_from_collapsed.py](https://github.com/Magdoll/cDNA_Cupcake/blob/81b7e7f6aeb53e15c11dd30a68a498a58e5f390a/annotation/make_file_for_subsampling_from_collapsed.py), and figured I could document them here since similar GitHub issues have helped me. ## Bug 1: Overestimating gene counts...
Hello there, I hope you're having an awesome day, and that all is going well on our side. I just wanted to reach out to you because I ran into...
Hi, I'm trying to use collapse_isoforms_by_sam.py as a part of a pipeline according to this paper: https://www.frontiersin.org/articles/10.3389/fgene.2021.683408/full ...with the following arguments: `python /cluster/projects/nn9244k/for_adam/lophius/cDNA_Cupcake/cupcake/tofu/collapse_isoforms_by_sam.py \ --cpus 6 -b ../mapping/minimap2_mapping/all_samples_polished.hq.highQual.mapped.bam --dun-merge-5-shorter -o...
I am trying to use fusion script and then sqanti3_qc and finally trying to classify the fusions similar to your tutorial (https://github.com/Magdoll/cDNA_Cupcake/wiki/Best-practice-for-fusion-transcript-finding). But at the end its not working. ##...
lima --isoseq --dump-clips -j 1 skera.bam primers.fa lima.bam | 20221108 08:24:16.804 | WARN | Unknown read type 'SEGMENT', will generate use SubreadSets! and no bam output !
Hello， When I run collapse_isoforms_by_sam.py with a big .sam file (~90GB), it ran quite slowly and always ended with an error 'OUT_OF_ME+ 0:125'. Are there any way I can optimize...
