-
Is 3_train.ipynb pointing to the wrong input file? The following input gives an error on bedtools command despite the bedtools command exists
```python
bw_file = grelu.data.preprocess.make_inserti…
-
Hi,
I've been puzzled by the lack of calls/site for CHG and CHH methylation for a few days now. I called similar data with Megalodon and modbamtobed a year or two ago and got very different results…
-
I and @valerianilucrezia were discussing with @caravagn about what would be useful for the `simulate_seq` function to return.
As today, it returns only the sequencing results, but we feel like it w…
-
#### Summary:
When calling the report for specific runs with the --run_results argument, a single value for the length of alignment is given in the alignment length column. However, the lengths of th…
-
Hi,
I was wondering if decoil currently supports the t2t reference genome?
I used decoil on the same sample with the grch38 and then the t2t reference genome. The grch38 reference gave the expe…
-
Hi, I aligned the transcript to the reference genome, and based on the coverage of reads, I found two alternative splicing events. However, the GTF file expanded by IsoQuant shows only one transcript …
-
Not sure if this is related to the similar post re: pbcstat, but it dumps core on me:
pbcstat *.paf.gz
Program starts
[M::aa_pb] collecting positions from paf file
[M::aa_pb] calculating cover…
-
Hi Lucas,
Many thanks for this awesome tool and fantastic documentation. I have one issue regarding the behaviour of --filter-mask-bed parameter. I will use a test example to show what I mean.
I…
-
Hello. I ran purge_dups successfully up through (including) the get_seqs step. See results from my slurm output file below. Both .hap.fa and .purged.fa files were produced but they are smaller than wh…
-
Thanks for this awesome tool
I am working on a Tetraploid plant with an estimated genome size of around 1.2 Gbp. So when I run Genomescope on my data with K 21, ploidy 4 and Average k-mer coverage…