cDNA_Cupcake
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Magdoll
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
Hello- I just wanted to make a note of two slight bugs I found while doing rarefaction analysis: 1. The script make_file_for_subsampling_from_collapsed.py doesn't work when the --include_single_exons flag is included...
I'm having similar problems to an issue from 2017 (duplicate isoforms in chain_samples.py output), where I'm seeing duplicate isoforms in the output of chain_samples.py, however the isoforms are all multi-exon...
Can you possibly add support for gzipped fastq and fasta files for `collapse_isoforms_by_sam.py`? It's a big difference in file size and it would be nice to be able to use...
Summarized results of by_loci/ to summarized.isophase_results.txt. ``` Traceback (most recent call last): File "./software/cDNA_Cupcake-master/phasing/utils/collect_all_vcf.py", line 14, in for r in reader: snps_by_chrom[r.CHROM].append((r.POS, r)) File "./software/anaconda2/lib/python2.7/site-packages/vcf/parser.py", line 586, in next samples...
Currently, `collapse_isoforms_by_sam.py` accepts a `-i` identity threshold, but that is the average identity over the whole alignment. Importantly, I want to add a per-exon identity threshold to filter out cases...
- [ ] integrate fusion finding into cupcake - [x] allow chaining of fusion transcripts
artifacts are present in Iso-Seq data often due to library preparation (template switching, PCR chimeras) that are difficult to remove because they come from the cDNA level (and not at...
Hello, I have recently encountered some difficulties when using SQANTI3 and cDNA_Cupcake. For some reasons, I need to use SQANTI3 and cDNA_Cupcake at the same time. I installed SQANTI3 and...
Hi. I went through the latest isoseq pipeline (v4.1.1) to run an inoseq experiment. I have started with a single bam files containing 3 samples did all the steps and...
Hello, I have been using fusion_finder.py to find a fusion gene recently, however, there is an error, how can I fix it, thank you for your help ![Uploading 微信图片_20240303175001.png…]()