Shian Su

I've hacked it myself and introduced a ```cpp int index_nodb_main(int argc, char** argv) { parse_index_options(argc, argv); // Read a map from fast5 files to read name from the sequencing summary...

Thanks @jts. The reason for what I'm doing is because I noticed that even with 16 threads allocated, the cluster reports less than 70% CPU utilisation, this is with new...

I believe it was aligned back to assembled contigs, so the read itself would have informed the contig sequence.

I'd like to pop up a tooltip locked to the mark without following the cursor. Is this possible right now?

True, it should be detectable from the sequences. I've written a preliminary implementation for guessing the barcode and UMI lengths based on the first read. ``` std::pair get_bc_umi_lengths(string bam_fn) {...

This is currently an issue with non-ENSEMBL annotations, are you using a non-ENSEMBL annotation?

Did you put that into the `annofn` argument? For the annotation you should be using a GFF3 file from ENSEMBL, so in your case you can download `ftp://ftp.ensembl.org/pub/release-91/gff3/mus_musculus/Mus_musculus.GRCm38.91.gff3.gz` and unzip...

Interesting idea, I could have a think about how to implement it. The core of scPipe was originally pure C++, which is why everything tended to be file-based. Fundamentally what...

Had a look using `rtracklayer::import()` unfortunately the issues that made me write the source specific code still persist, though it may alleviate some complexity with regards to GFF3/GTF/BED. # ENSEMBL...

Some support incoming: https://github.com/Shians/scPipe/commit/02517ab46a09efae6a48c365dee7c5ca842d5da6 So the goal is to generate a SAF style data.table (http://bioinf.wehi.edu.au/featureCounts/). I've written up helper functions to import different annotation formats, the major upside of using...