Nadia Davidson

Use own clustering

1

Hi, I would like to use clustering that's come from another source, and just use RATTLE for the error correction and polishing. Is this possible? If so, what format and...

Bug in Stage index_bams

2

index_complete.txt can't be found (but is placed in the working directory). replace exec "touch index_complete.txt" with exec "touch $output.dir/index_complete.txt" in clinker.pipe ?

> source("https://bioconductor.org/biocLite.R") Error: With R version 3.5 or greater, install Bioconductor packages using BiocManager; see https://bioconductor.org/install Hope the above makes sense.

See https://groups.google.com/forum/#!topic/corset-project/lCRQT0lUfgA

Replace gmap with minimap2 in align_contigs_against_genome

2

Many false positives seem to be a result of poor alignment of contigs to the genome, which are resulting is bad annoation. e.g. k49_1134199 0 chr21 44220603 3 281S16M6810N5M2435N6M6199N13M50029N16M1I6M32I32M21I4M4911N3M16052N8M8047N10M2202N2I11M1I25M3I22M6D11M750N10M1163N4M1809N3M1264N7M24156N4M6825N5M3920N2M12899N7M4539N3M7819N8M10199N7M1D1M4453N8M5667N2M11730N3M55386N4M402730N2M6445N3I6M15389N1M13514N9M1I47M2N4I126M15D1279M *...

In the stage that aligns superTranscriptome against each other.

-p assemblyFasta= line in params.txt

4

-p assemblyFasta= in params.txt being interpreted with non-empty value. Makes the pipeline assume that an assembly has been provided. Tried setting to '',"","\'\'" etc. but that wasn't interpreted correctly by...