I used the parameter --bed with circAtlas bed file, the outputs are always "KeyError: '[circAtlas ID]'"

[DooYal]

Though I deleted the record as the bug report mentioned, it always interrupts with error report like the image, so how should I do can quantify the sequence with circAtlas ID.

[DooYal]

我的输入是==================================== CIRIquant -t 20 \ -1 $out_prefix.qc.1.fastq.gz \ -2 $out_prefix.qc.2.fastq.gz \ --bam $out_prefix.tp2.fusion/accepted_hits.bam \ --config ${config_yml} \ --bed ~/transcirc/human_circ_v3.0.bed \ -o $out_prefix.ciriquant \ -p $sample.ciriquant

config_yml=================================== tools: bwa:~/miniconda3/envs/circ/bin/bwa hisat2: ~/miniconda3/envs/circ/bin/hisat2 stringtie: ~/miniconda3/envs/circ/bin/stringtie samtools: ~/program/samtools-1.19.2/bin/samtools reference: fasta: ~/humandb/G38.p14.fasta gtf: ~/humandb/gencode.v44.annotation.gtf bwa_index: ~/humandb/G38.p14.bwa hisat_index: ~/humandb/G38.p14.hs2

[Kevinzjy]

Hi @DooYal , the input file should be converted to standard bed format, for example:

chrom    start    end    circRNA_ID    .    strand

[DooYal]

Hi @DooYal , the input file should be converted to standard bed format, for example:

chrom    start    end    circRNA_ID    .    strand

是这种格式的，也是制表符分割，但是总会在一个点报错，去查了一下报错的地方和其它行文本没有区别