xTea
xTea copied to clipboard
parklab
Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ Command line :path-to-dir/xTea-master/bin/xtea -i normal_name.csv -b normal_name_bam.csv -x null -p ./normal_wes/5.TE_output/ -o ./normal_wes/5.TE_output/multiple_TE_output.sh -l path-to-dir/xTea-master/rep_lib_annotation/ -r ~/db/human_genome_index/hg38/hg38.fa -g path-to-dir/xTea-master/gencode.v33.hg38.annotation.gff3 --xtea path-to-dir/xTea-master/xtea/ -q short -f 1 -y 7 -n 8...
Hi, We wanted to try xTea on a plant species. Is that possible or does it require a human reference? Agnieszka
Hello and thank you for sharing this tool. I ran xtea_long, per the instructions on the xtea_long branch, on Pac Bio data. The final output was only txt files. Is...
Question from https://github.com/parklab/xTea/issues/20 > Hi, I tried using >5900bp as the cutoff for the full length L1. I run hg38 first to see whether I can reproduce the result in...
Hi, I am facing a problem in identifying "pseudogenes" insertion from pacbio reads; I am using the following command: python3 xTea/bin/xtea_long -i sample_id -b bam -r GRCh38_latest_genomic.primary.fa -g GRCh38_latest_genomic.gff --xtea=tools/xTea/xtea_long...
Hi, Thanks for your great tools! I am running version xTea=0.1.6 installed using conda and installed short reads with the latest version by "git clone https://github.com/parklab/xTea.git" we generate the running...
Running with SLURM, looks like email is still set: ``` #SBATCH [email protected] ``` Would be nice to have -e option for email. Thanks, Phil
Hi! In the Nat. Comm. paper (2021) you mention that: "For datasets consisting of Illumina short reads and long reads, candidates from Illumina short reads are merged with candidates from...
Hi thank you for developing great tool! I am a beginner in these analysis. I am using nanopore data, but the analysis stopped for more than 24 hours during the...
Hi Simon, For me the Docker image does not build from Dockerfile the way it is. I updated Dockerfile to use current Debian stable instead of Ubuntu 16.04. Hopefully I...
