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parklab / xTea

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics
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Dockerfile: RUN rm -rf xTea #126

Closed minw2828 closed 3 months ago

minw2828 commented 3 months ago

Hello,

Thank you for developing the tool.

I am wondering why you need to have the line 55 of code in your Dockerfile. 55 RUN rm -rf xTea

I thought to run the following step, one would still need xTea/bin/xtea or xTea/bin/xtea_long?

xtea --case_ctrl --tumor -i sample_id.txt -b case_ctrl_bam_list.txt -p ./path_work_folder/ -o submit_jobs.sh -l /home/ec2-user/rep_lib_annotation/ -r /home/ec2-user/reference/genome.fa -g /home/gene_annotation_file.gff3 --xtea /home/ec2-user/xTea/xtea/ -y 7 -f 5907 --slurm -t 0-12:00 -q short -n 8 -m 25

Many thanks, Min

simoncchu commented 3 months ago

Hi, the docker file is for germline TE insertion identification, not for somatic. You can revise according for a somatic one.

minw2828 commented 3 months ago

Hello @simoncchu,

Thank you for your quick reply!

I have some long read data with N/T match. I'd like to do germline and somatic genotyping, and case-control analyses. Which branch and workflow should I go with?

Many thanks, Min

simoncchu commented 3 months ago

For long reads, we don't have a case/ctrl mode right now, although you can run separately on the case and ctrl with the long-read branch: https://github.com/parklab/xTea/tree/xTea_long_release_v0.1.0