cDNA_Cupcake
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Magdoll
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
`collapse_isoforms_by_sam.py --input HL60_fltnc_dedup.fasta -s HL60_fltnc_dedup.fasta.sorted.sam -c 0.99 -i 0.95 --gen_mol_count -o HL60_fltnc_dedup.5merge &` [1] 41376 (SQANTI3.env) [/home/ubuntu/Yale_PacBio_Data/isoseq_single-cell_analysis] Traceback (most recent call last): File "/home/ubuntu/miniconda3/envs/SQANTI3.env/bin/collapse_isoforms_by_sam.py", line 4, in __import__('pkg_resources').run_script('cupcake==28.0.0', 'collapse_isoforms_by_sam.py') File...
Hi, I used the same pipeline with the @kmattioli to process the isoseq data, but i met an error when running demux_isoseq_with_genome.py. The closed issue is in the link https://github.com/Magdoll/cDNA_Cupcake/issues/167#issue-947981042...
Hello, This the first time I am using Cupcake to handle IsoSeq data. I am trying to collapse HQ isoforms from IsoSeq reads (FASTA file) with collapse_isoforms_by_sam.py but it fails....
Hi, I was trying to use IsoPhase do call SNPs from the Pacbio Isoseq data for a single sample. However, when I run the `select_loci_to_phase.py `with all the files required,...
Does **collapse_isoforms_by_sam.py** have an upper limit to the inter-exon distance it will collapse into a putative isoform? In my animal model, I have a wildtype allele that spans about 154...
Hi! when i merged my all sample,the error that " Expects to see tmp_roots_3-2.0.gff,tmp_roots_3-2.0.mega_info.txt,tmp_roots_3-2.0.group.txt but one or more files are missing! Abort! " was appeared.But tmp_roots_3-2.1 tmp_roots_3-2.4 tmp_roots_3-2.6 were got.This...
Hi, I am trying to chain 3 samples. However, I keep getting the following error: `Exception: Sanity check failed! Please make sure the PBIDs listed in collapsed.gff are also in...
Hi Liz, I'm using chain_samples.py on 6 human samples. The 6 samples were multiplexed and run over 6 SMRTcells and samples were combined after the refine step. After the collapse...
Hi Liz, Apologies if this is a redundant question - I think #7 might explain the results I'm getting too, but wanted to double check. I'm chaining together some iso-seq...
