poonchilam

outputting error

2

Hi there, I was trying to train my own basecaller, here's what i did - ``` # index ground truth sequences minimap2 -x map-ont -d groundtruth/groundtruth.mmi groundtruth/gt.fa # basecall and...

Hello! I am new to nanopore signal processings and I was trying to run the MotifSeq in SquiggleKit. However each time I ran scrappie `scrappie squiggle my_kmer.fa > scrappie_kmer.model` I...

ERROR: basic_string::substr

3

Hi Kishwar, I got these errors when I ran singularity pepper on a mouse dataset (output bam file from Sockeye): ``` [09-24-2022 17:30:09] INFO: ONT VARIANT CALLING MODE SELECTED. [09-24-2022...

Add query to ref coord mapping

2

targeting spliced read issue https://github.com/nanoporetech/remora/issues/118#issue-1925040269

ref to signal mapping did not consider splicing

5

Hi @marcus1487, I was using remora API on real direct RNA-seq data, but ran into errors from this command: ```python io_read = Read.from_pod5_and_alignment( pod5_read_record=pod5_reads[bam_read.query_name], alignment_record=bam_read, reverse_signal=True, ) ``` ``` ---------------------------------------------------------------------------...

Automatically detect all chromosomes in bam

2

Hi there, I ran cellsnp on my mouse data but ran into this error: ``` [W::check_args] Max depth set to maximum value (2147483647) [I::main] mode 2b: pileup 22 whole chromosomes...

update seurat5 count matrix access

1

updated seurat5 count matrix access. After some testing, it's working well with the basic examples from the vignette.