Rascaf
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mourisl
Scaffolding with RNA-seq read alignment
I am trying to improve the scaffolding on a genome assembled using Supernova and Chromium 10x. I've aligned my reads to the genome using hisat2 and used samtools to sort/convert...
Hi, I used TopHat to align my RNAseq PE reads. I'm getting absolutely no improvements on the final assembly, and I'm suspicious that I'm doing something wrong, because I did...
Hi, I'm trying to apply Rascaf to an assembly that is unpolished and has high base level errors. I still want to try out Rascaf, and I was wondering if...
Good afternoon, I am trying to run rascaf to improve a draft genome that I am working with. However when I try to use it I get the following error...
Hi, I used rascaf like this: `rascaf -b Aligned.sortedByCoord.out.bam -f draft.fa ` but I got the following error: ``` Found 135172 exon blocks. Assertion failed: (readCnt > 30), function GetAlignmentsInfo,...
Hello, In the manual it mentioned an optional step of validating proposed connections by mapping to a public protein database. I think this is really a great idea, but I...
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)...
rascaf-join uses the output from rascaf to determine whether the assembly was contig level and access the input assembly fasta file. It does this by searching for "-f" in the...
Hello, I am running rascaf but in rascaf-join it stays for ever and no output is generated. I can see with top that it is running. this is the run...
Hi Li Song, I enconter a problem when run rascaf-join. (See bellow) The genome is approxmately 1G, bam file 2 G. How to adjust it? Thanks [lzc@localhost lotusbam]$ /home/lzc/CJM_reseq/rascaf/rascaf-join -r...
