Shujun Ou

Install via singularity

7

Hello, I don't have `sudo` privileges on our HPC platform, so I could not use the `docker` nor the regular installation method. Instead, I am trying to install `tephra` via...

LAI does not improve despite sequencing and assembly improvements

21

Dear shujun， First of all apologize for my bad English. I have sequenced dozens species, these species belong to the same genus (eg. wild, cultivars, landrances), and I will construct...

[version] gt.1.5.3 LTRharvest [parameters] gt ltrharvest -index Bond -minlenltr 100 -maxlenltr 7000 -mintsd 5 -maxtsd 5 -motif TGCA -motifmis 0 -similar 90 -vic 40 -seed 40 -seqids yes -out Bond.ltrTE.fa...

When I aligned two maize genomes, the paf file contained incomplete lines that will convert numeric columns to characters, then the script crashed becasue it was not expecting characters. I...

Slow input file conversion

4

Hello, Thank you for developing STITCH. It looks like a very promising program with better performance to impute rare variants. I was trying to use it on a rice population...

Loss of resolution

9

Hello, Thank you for implementing this great pipeline! I successfully ran it but I saw the resolution of output is much lower than the original input. The loss of resolution...

Huge memory consumption

4

Hello, I want to use `hs-blastn` to search in a genome with size **~2 GB** (i.e., the maize genome), the indexing was not fast but no error reported. When I...

Make bed file for reads processed by primrose

8

Hello, I am trying to find out the methylation status of haplotype-specific variants. These variants may not be assembled in the haploid genome (no mapping) and thus I need to...