Richard Corbett

cudamapper error using bam output

2

Hi folks, I'm trying cudamapper with this command: `/opt/GenomeWorks-2021.02.2/bin/cudamapper PAG33026_pass_concat.fastq.gz ../hg19a.fa -B > cudamapper_2021_02_02_GM24385.bam` which outputs quite a lot of output to stdout/stderr, from which I have reported the unique...

Hi again. With this command I get 77 fastas returned: `ncbi-genome-download -t 64187 -F fasta,assembly-report -l complete all --flat-output -H` I was hoping to see a way to select for...

Hi there. I made a number of random samplings of the full microsatellite list created with "scan". I am downsampling it to test if using a subset of the positions...

1.3.2 read group - can use only 1?

1

**Is your feature request related to a problem? Please describe.** I have samples that are sequenced deeply and the data span multiple nanopore flowcells. When I merge those bams there...

help undestanding output

13

Hi dropseqpipers, I have downsampled some single cell data to test for the quality of the results using the same number of reads per cell. I have given each of...

First test with Dolomite Nadia data

9

Hi folks, I'm trying dropSeeqPipe for the first time on some test Nadia data we generated. I am using the example Nadia template config and I have 4 samples, each...

Hi folks, I am using 2.9.10 and found that when I provide a bed file to --callregions in the somatic workflow I need to be careful to format it appropriately....

preserve timestamp during bam->cram

4

Hi folks, Is it possible to preserve the timestamp of the original BAM file when creating a CRAM? thanks Richard

is there a container?

2

Hi folks, Is there a docker or singularity container available for me to run speedseq sv? thanks, Richard

trouble processing minimap alignments from guppy

12

Hi there. I am using guppy to basecall my ONT data and recently I started testing the option for it to create a bam that contains methylation data. The bam...