Philip Lijnzaad

Add support for output to BAM

10

I just fixed the File Not Found (issue #86) a bit (see my pull request), but whereas it seems to now be able to read sam and bam files, it...

Dear Sean, CHETAH has been published in Nucleic Acids Research, doi: 10.1093/nar/gkz543 Cheers, Philip

The latest RefSeq data set from UCSC has 12 transcript whose start seems to equal 0. This causes gffread (version 2.2.1) to crash without any warning. It would be nice...

Is there a way to label edges?

1

Hi Luke and/or others, is there an easy way to label the edges, specifically with the numbers or percentages distributing over the finer-clustered nodes under it? If not, I'd like...

parameter sweeping the k parameter?

3

Thanks for this wonderful tool! I have been looking for a way to conveniently/cheaply 'parameter-sweep' _k_, but could not find it. I.e., whenever possible I use `--skip_remap` to avoid remapping...

Dear Haynes, thanks for your super useful tool. I'm getting the following error when running souporcell: ``` souporcell_retag_tmp_6.bam.err:Traceback (most recent call last): souporcell_retag_tmp_6.bam.err: File "/opt/souporcell/retag.py", line 37, in souporcell_retag_tmp_6.bam.err: assert...

Truseq Read1 and mixed single/dual demultiplexing

9

Dear Xi, many many thanks for this brilliant resource! I had one question: on https://teichlab.github.io/scg_lib_structs/methods_html/Illumina.html, the 'Truseq Read1' sequences under 'Truseq Single Index Library' and 'Truseq Dual Index Library' differ...

This PR implements the import of STAR-Fusion+FusionInspector output in order to get a `plotFusionReads`-like plot. FusionInspector creates a virtual 'mini genome' to which the fusion reads are again aligned. Unfortunately,...

Import fusion inspector support

2

I had hoped that Chimeraviz could also do a `plotFusionReads` type plot with output from STAR-Fusion+FusionInspector, but that is unfortunately not the case, the data is too different. It turns...