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                                            mvheetve

Manta cannot detect same chromosome large deletions

Hi, we used Manta for SV calling on WGS data (30-40x). Two cases should have large deletions as already picked up by other sequencing and PCR efforts, but neither of...

Manta cannot detect same chromosome large deletions

> > I found my solution,I have set target bed file,when drop this parameter,we got the large deletions and translocations > > […](#) > > ---- Replied Message ---- |...

SVIM 2.0.0 in conda

Hi there, any update on this?

Assembled transcripts lack canonical transcript, clearly visible in the alignment

Adding to that. I ran StringTie in short-read mode (not using params `-R` or `-L`), with the following command `stringtie $f -o $dir/${x##*/} -f 0 -t` which yielded the output...

TypeError: tuple indices must be integers or slices, not str

Hi there, exact same error here, on all submitted jobs. Using `AlphaFold/2.3.4-foss-2022a-CUDA-11.7.0-ColabFold`. Command: ``` alphafold \ --fasta_paths=${input} \ --max_template_date=2023-03-10 \ --db_preset=full_dbs \ --data_dir ${ALPHAFOLD_DATA_DIR}\ --model_preset=multimer \ --output_dir ${outdir} ``` Error:...

Salmon strand inference is often wrong

Hi there, I'm seeing behaviour, which could be similar to your issue, in data I received from several collaborators. The logs show for example: `Please check MultiQC report: 17/47 samples...