aaannaw

Hello I have used svim-asm to identify SVs between two genome assemblies from two species. I got the most largest INV variant is 96691, however I got the most largest...

sparseToDense.py error

2

Hi When I use sparseToDense.py to convert HiC-Pro output into dense format: python 00.sparseToDense.py -b Ma_40000_abs.bed Ma_40000_iced.matrix --perchr. The first row and column of the output result of Chr1 (Ma_40000_iced_Chr1_dense.matrix)...

How to select positive signals of the foreground branch from the results of aBSREL modle

3

Hello, professor I am running` hyphy aBSREL --alignment 00.input/evm.model.Chr10.103.cds.fa --tree 00.root.tree --branches FG --output 01.aBSREL/evm.model.Chr10.103.json > 01.aBSREL/evm.model.Chr10.103.log 2>&1` for orthologous genes of six species. Then I got the output file-*.json...

Hello，professor I am running segalign image using singularity but I occurred the headache error as follwing.  Could you give me any suggestions! Best wishes! Na Wan

Hello I am running mafToFastaStitcher command with test data: `/data/01/p1/user157/software/mafTools/bin/mafToFastaStitcher -m input.maf --seqs input.fa --breakpointPenalty 5 --outMfa output.mfa` The input.maf is: ``` ## maf version=1 a score=0.0 `status=test.input` s ref.chr1...

how to interpret the output plot

5

Hello,Professor I downloaded the TOGA result file for several species from https://genome.senckenberg.de/download/TOGA/mouse_mm10_reference/Rodentia/. I focused on a gene ENSMUSG00000057170 and the gene is showed loss status in the loss_summ_data.tsv file. The...

The number of tasks submitted by SLURM exceeded the limit

16

Hello, professor I was running the pipeline to align my genome assemblies with mm10 genome via slurm: ` ./make_chains.py target query mm10.fasta Bsu.softmask.fasta --pd mm-Bsu -f --chaining_memory 30 --cluster_queue pNormal...

substr outside of string at /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl line 129

1

Hello, I am running LTR retriever, and I am coming across these errors: `/data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/get_range.pl 1 LTRretriever.genome.fna.retriever.scn LTRretriever.genome.fna -f -g -max_ratio 50 /data/00/user/user101/software/LTR_retriever/LTR_retriever/bin/call_seq_by_list.pl LTRretriever.genome.fna.retriever.scn.full -C LTRretriever.genome.fna substr outside of string at...