Annoted 0 fusion junction

[JerryZhang-1222]

hello sir！First thanks a lot for providing a fantanstic tool for circRNA identification! I have an issue about the annotate step: all of the output files are empty. I checked my bed files and they all seem to be right, and the genepred file for Rattus which I made by myself is also in the correct position. Also I noticed that some of the donor sites and the accepter sites in the bed files are almost corresponed to the exon start sites and end sites in the genepred files but missed a few hundreds of bps and that made my very confused.

here is the log file:

CIRCexplorer parameters: /home/zhangfy/miniconda3/envs/RNAseq/bin/CIRCexplorer2 annotate -r /home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/4_annotate/Rattus.genepred -g /home/zhangfy/data_projects/RNAseq/LW_MPP/reference/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa -b /home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/3_parse/6_back_spliced_junction.bed -o 6_circularRNA_known.txt Start CIRCexplorer2 annotate at 00:13:48 Start to annotate fusion junctions... Annotated 0 fusion junctions! Start to fix fusion junctions... Fixed 0 fusion junctions! End CIRCexplorer2 annotate at 00:13:51

here are the first few lines of one of the bed files:

MT 15477 15689 FUSIONJUNC_0/2 0 + 19 32562077 47681809 FUSIONJUNC_1/1 0 + 1 44056455 44077618 FUSIONJUNC_2/1 0 + 6 76200504 76205352 FUSIONJUNC_3/2 0 + 5 91136795 91136896 FUSIONJUNC_4/1 0 + 5 91128426 91128652 FUSIONJUNC_5/2 0 + 16 8883292 8883871 FUSIONJUNC_6/1 0 + 13 67311522 67312186 FUSIONJUNC_7/1 0 + 13 95128659 95348984 FUSIONJUNC_8/3 0 + 11 38351756 38352109 FUSIONJUNC_9/1 0 + X 65291486 65295744 FUSIONJUNC_10/2 0 + 8 68647568 68647772 FUSIONJUNC_11/1 0 + 13 7179473 7179726 FUSIONJUNC_12/2 0 + 3 174787719 175367022 FUSIONJUNC_13/1 0 + 9 113516802 113518802 FUSIONJUNC_14/3 0 +

and here is my code:

#!/bin/bash
cat files.txt | while read id;
do echo $id
        arr=($id) 
        sample=${arr[0]}
        ref_dir=/home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/4_annotate/Rattus.genepred
        fa_dir=/home/zhangfy/data_projects/RNAseq/LW_MPP/reference/Rattus_norvegicus.Rnor_6.0.dna.toplevel.fa
        bed_dir=/home/zhangfy/data_projects/RNAseq/LW_MPP/circ_RNA_proj/3_parse/${sample}_back_spliced_junction.bed
        nohup CIRCexplorer2 annotate \
                -r ${ref_dir} \
                -g ${fa_dir} \
                -b ${bed_dir} \
                -o ${sample}_circularRNA_known.txt> annotate.log 2>&1 &
done

I've attahced all of the files mentioned above:

1. back_spliced junction.txt is one of the output bed files after the parsing step.
2. annotate.log is the log file.
3. annotate.txt is my bash script while the files.txt is a namelist that will be needed in the bash script.
4. Rattus.txt is the reference genepred file. 1_back_spliced_junction.txt annotate.log annotate.txt files.txt Rattus.txt

Thanks again! Zhangfy

[kepbod]

The chrom column in your back_spliced junction file did not have 'chr', but your Rattus.txt had. Please make sure they are consistent.

[JerryZhang-1222]

The chrom column in your back_spliced junction file did not have 'chr', but your Rattus.txt had. Please make sure they are consistent.

Thank you! That perfectly soved my problem!