cDNA_Cupcake
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Magdoll
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
Hi! Thank you for your package! I am trying to use collapse_isoforms_by_sam.py as part of another pipeline (https://github.com/Gaius-Augustus/BRAKER/blob/master/docs/long_reads/long_read_protocol.md). The main problem is that your test_data/hq_isoforms.fastq.sorted.sam is quite different from mine...
After the update on 28 August, the cupcake2 directory disappeared but it is still required for the installation of cupcake (see setup.py file).
Hi I am trying to use "chain_samples.py" from your package script after post collapsed step of cDNA. Here i am using three different mappers out from cDNA and the config...
This PR adds parallelization to subsampling as this script takes too long to run right now. I tested new script with 10,000 total reads at 100 reads step size and...
Hi, I tried get_abundance_post_collapse.py cDNA_Cupcake/cupcake/test_data/test.collapsed cDNA_Cupcake/cupcake/test_data/cluster_report.csv **My output:** *test.collapsed.read_stat.txt* id is_fl stat pbid m64012_190727_053041/105120134/ccs Y unmapped NA m64012_190727_053041/21628950/ccs Y unmapped NA m64012_190727_053041/114950281/ccs Y unmapped NA m64012_190727_053041/87229073/ccs Y unmapped NA m64012_190727_053041/153355478/ccs...
Hi, I'm trying to run the chaining script, and I'm curious where the count.txt file come from: SAMPLE=; SAMPLE=; GROUP_FILENAME=touse.group.txt GFF_FILENAME=touse.gff **COUNT_FILENAME=touse.count.txt** FASTQ_FILENAME=optional.rep.fastq I ran the collapse script and so...
I am interesting in the fusion_finder.py and hope to find the true positive fusion transcript, however, I am struggling for a long while to find other evidences to support the...
Hi, Magdoll, I have download the [fusion fasta](http://datasets.pacb.com.s3.amazonaws.com/2015/IsoSeqHumanMCF7Transcriptome/IsoSeq_MCF7_2015edition_polished.fusion.fasta) file and used the same commands and parameters at (https://github.com/Magdoll/cDNA_Cupcake/wiki/Best-practice-for-fusion-transcript-finding) 1) minimap2 against hg38 & sort 2.) fusion_finder.py , 3.) SQANTI (gencode.v33)...
Hi, Liz, I have found that when run the collapse with some data was very slow, most of the time it won't running finish (kill the process by myself after...
Hi, I was hoping someone could help me solve/clarify the issue I'm having below. First, I am running cDNA_Cupcake v28.0.0, taken from README: # cDNA_Cupcake Last Updated: 09.15.2021 Current version:...
