Simone Maestri

Dear Fritz, I tried to filter out SVs occurring in assembly gaps, represented in bed format, using `SURVIVOR filter`. I noticed that some SVs partially overlapping a gap were not...

Dear developers, I'm running dena on a dataset, and I am not able to get any results. In particular, I noticed that this command: `python3 /DENA/step4_predict/LSTM_extract.py predict --fast5 FAST5_dir --corr_grp...

Consensus sequences disagree with predicted numbers of repeats

4

Dear tandem-genotypes developers, I am using tandem-genoypes v1.8.3 to obtain consensus sequences for the two alleles. After running the alignment with last, I am running: ``` tandem-genotypes -v -o2 $TARGET...

Dear Pavian developers, I am facing some issues while trying to install the tool. Inside R v3.5.1 I am running: `remotes::install_github("fbreitwieser/pavian", force=TRUE)` These are the error messages I get: >...

### Description of feature Dear developers, in [cellranger manual](https://www.10xgenomics.com/support/software/cell-ranger/latest/analysis/inputs/cr-3p-references/), it is reported that parameters `--genome`, `--fasta` and `--genes` of `cellranger mkref` can be specified multiple times, for each of the...

OSError: [Errno 7] Argument list too long

7

Dear Breakseq2 developers, I am trying to run the software through SVE (https://github.com/TheJacksonLaboratory/SVE) wrapper on a BAM file obtained aligning sequence reads to hg38 reference (with alternative haplotypes). However, I...

bam.routed file is empty

12

Dear Hydra developers, after making hydra configuration (make_hydra_config.py) and extracting discordants for sample0 (extract_discordants.py), I run command for routing all samples into hydra router (hydra-router). This command doesn't give any...

Hi, I tried to use the `ema align` command to have barcoded reads aligned to a reference. However I got this error: > BWA initialization... > [M::bwa_idx_load_from_disk] read 0 ALT...

IGV visualization of bedMethyl file

4

Dear all, I would like to know if there is a way to properly visualize methylation information obtained from modkit in IGV genome browser (testing IGV 2.17 snapshot). In particular,...

Sequence strand bias in ~600 bp repetitive regions

5

Dear Dorado developers, we have PCR amplicons of a mouse genomic region encompassing Htt exon 1, which includes a repetitive region with about 200 CAG repeats, showing some length variability...