Cogent

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execution error with reconstruct_contig.py FileNotFoundError: [Errno 2] No such file or directory

4

Running cogent 6.0.0 / reconstruct_contig.py I got such error on several cluster for which reconstruction failed using kmer 30, 60 and 80: un example below: jleple@genologin1 /work/jleple/PACBIOII/E656_SMRTCell_A/COGENT_A $ cat slurm-19002922_10.out...

jcleple33

Getting unassigned sequence IDs

1

Hello, The code for getting the unassigned IDs in the [tutorial](https://github.com/Magdoll/Cogent/wiki/Tutorial:-Using-Cogent-to-collapse-redundant-transcripts-in-absence-of-genome#getting-the-unassigned-sequences) does not seem right: ``` tail -n 1 test_human.partition.txt | tr ',' '\n' > unassigned.list # Outputs the last...

bruvellu

Will I able to run Cogent on RNAspades output?

2

I've run Cogent on my iso-seq run and got really got results. short illumina reads map to it at ~65% alignment and I get a busco completeness score of 65%...

maorkn

Hi :) I'm running Cogent for a large dataset and `run_preCluster.py` outputs a `preCluster_out.tucked.fasta` file. What are these transcripts? I had a look in the Cupcake code but couldn't figure...

bruvellu

reconstruct gene longer in 3 prime than associated isoforms

3

Hi! Running Cogent on isoseq3 data, after collapsing and filtering for 5' degraded isoform and reconstruction I have aligned the reconstructed gene and the different hq_isoforms. I do not understand...

jcleple33

Just wanted to share my updated sh script which automatically tries to re-run the failed contig construct mode. It tries until kmer 99, after that it copies the input fasta...

HenrivdGeest