MarieLataretu

Hi, I still have the problem, that bowtie2-build does not create rev files and/or produces segmentation faults. Here are the versions I tested: - version 2.2.9 (conda create -n bowtie2-broken...

Hi, this is the input fasta (unzipped): ``` ftp://ftp.ensembl.org/pub/release-92/fasta/mus_musculus/dna/Mus_musculus.GRCm38.dna.primary_assembly.fa.gz ``` here we add 'chr' to chromosomes as prefix: ``` sed -r '/^>/ s/>([1-9MXY])/>chr\1/' Mus_musculus.GRCm38.dna.primary_assembly.fa > Mus_musculus.GRCm38.dna.primary_assembly.chr.fa ``` and this is...

Sure! the command is now: ``` nice /path/to/bowtie2-build-s-debug -t 20 /path/to/Mus_musculus.GRCm38.dna.primary_assembly.chr.fa bowtie2-index/Mus_musculus.GRCm38.dna.primary_assembly.chr.debug &> bowtie2-index/debug.log ``` and the resulting log file: ``` Settings: Output files: "bowtie2-index/Mus_musculus.GRCm38.dna.primary_assembly.debug.*.bt2" Line rate: 6 (line is...

Hi @corneliusroemer , many thanks for reporting this! Looking at the DESH data, it is most probably a (sequencing) lab bias. We are in contact with the lab.

Hi @corneliusroemer , thanks again for reporting! Here, it also looks like a (sequencing) lab bias in the DESH data. We are in contact with the lab.

Hi @AngieHinrichs, thanks for reporting this! We are in contact with the labs. I was able to reproduce T11524C & A11537G with raw BA.5 data and the unmodified primer file....

Reminds me of this issue https://github.com/nanoporetech/medaka/issues/351, and the BAM looks very similar 

Back in January, it was also S:69/70 > When you look at the unaligned/original FASTA sequence, it seems like that instead of a single '-' at deletions to indicate a...

I didn't had time to look at the frame shift sequences (and metadata) data in DESH. There is only one sample sequenced at RKI with this frame shift (at least...