kyle

read 0 ALT contigs AND fail to open file "xxxx.clipped.fq"

9

+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ 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...

I don't konw how to set --variants parameter, and what's wrong with the following code: nextflow run main.nf --reads '/home/liukai/postd/msi_project/RNAseq1101/00.CleanData/C15*_RNA_{1,2}.clean.fq.gz' --denylist ~/db/human_genome_index/hg38/S1667195179_agilent_region.hg38.bed —variants /home/liukai/db/human_genome_inde x/hg38/hg38_VCF/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --results my_msi_results_newref --genome /home/liukai/db/human_genome_index/hg38/hg38_VCF/Homo_sapiens_assembly38.fasta -profile...

Can this tools be used for WES data

1

Can we detect TE from WES data using this software