Dietmar Rieder

I'd also be very interested in having that feature e.g. `--adapter_sequence_r2 NNNNNNNNNNAGATCGGAAGAGCGTCGTGTAGGGAAAGA` should remove an extra 10 bases Any planes to implement this? Trimgalore seems to support Ns in the...

Here is my use case: Notes from the Zymo-Seq RiboFree® Total RNA Library Kit: `The Zymo-Seq RiboFree® Total RNA Library Kit employs a lowcomplexity bridge to ligate the Illumina® P7...

The same applies to `umitools_extract_method` and `umitools_bc_pattern` Tested with version `3.8.1`

Hi, I just noticed that difference is huge. When I use recalibrated and indel realigned tumor/normal BAMs from a WGS sample, I get only 17 somatic SVs (somaticSV.vcf.gz). When I...

Oh... I just realized, that the difference is due to only using coding regions for making the realigned BAM file. Sorry.

Hello, thanks for your interest in `nextNEOpi`! unfortunately we do not support other organisms than `human` at the moment. In principle it could be possible to run `nextNEOpi` on mouse...

Hi, you are right it is v1.3.1. I attached the log obtained with -vv, if this is not enough, I can send you the data, let me know. [PureClip.log](https://github.com/skrakau/PureCLIP/files/3921286/PureClip.log)

Hi, I just wanted to ask if you did get my private message via filesender with the data? I sent it on Dec. 10 to your (?) University address.

Can you post the `vcf.gz` files from the c5 dir, e.g. create the `tar.gz` with the `--dereference` tar option.

It seems that you are lacking the `Frameshift.pm` and the `Wildtype.pm` plugins in `vep_cache/Plugins` . They should have been installed on the first run of the pipeline, see: https://github.com/icbi-lab/nextNEOpi/blob/fe7b21cdc0b97aae38195e5f5ac1b9851674f6b1/nextNEOpi.nf#L3255-L3291 Did...