BESST_RNA
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ksahlin
Scaffolding of genomic assemblies with RNA seq data
Dear @ksahlin When running a test case with 10M reads, that do not cover much of the genome, I seem to get a ZeroDivsionError similar to #3 . The contigs...
Hi, I mapped my RNA reads to my assembly with Hisat2 and fed it into BESST_RNA. However, I got the following error. ---------- Starting scaffolding with library: DARW_heart.hisat2.sorted.bam Parsing BAM...
Hi. I have several paired-end RNA libraries with different library statistics (insert size, read length [also various length each after trimming]). How can I input these in the tool? Does...
HI, I am working on a hybrid assembly for a 3.2G allotetraploid plant genome: 1. Illumina assembly with [w2rap-contigger](https://github.com/bioinfologics/w2rap-contigger). 2. [DBG2OLC](https://github.com/yechengxi/DBG2OLC) to combine Illumina assembly with PacBio reads 3. [PBjelly](https://github.com/alvaralmstedt/Tutorials/wiki/Gap-closing-with-PBJelly)...
Hi, part of the output generated is called -pass1. Does this imply there might be advantages to iterative scaffolding ? I haven't tried this yet, have you ? Also, I...
Mapper
Hi, maybe I missed this, but which aligner is recommended ? STAR or Tophat, or bwa, bowtie2 etc. Thanks, Colin