circRNA with only one base

[gudeqing]

Hi, I found the fantastic tool could be easily appied when I already got the ouput file C190476.Chimeric.out.junction of STAR. However, the final result surprised me for detecting one circRNA with only one base (the first record shown below), thus I think I got an issue:

CIRCexplorer2 parse -t STAR C190476.Chimeric.out.junction > C190476.CIRCexplorer2_parse.log
CIRCexplorer2 annotate -r hg38_ref.txt -g /nfs2/database/gencode_v29/GRCh38.primary_assembly.genome.fa -b back_spliced_junction.bed -o circularRNA_known.txt > CIRCexplorer2_annotate.log

cat circularRNA_known.txt: 
chr5    179623035   179623036   circular_RNA/4  1   -   179623035   179623035   0,0,0   1   1   0   4   ciRNA   HNRNPH1 NM_001364239    2   chr5:179621397-179623036
chr11   62855291    62855366    circular_RNA/7  0   -   62855291    62855291    0,0,0   1   75  0   7   circRNA SNORD26 NR_002564 None|None
chr7    44840898    44843354    circular_RNA/26 0   -   44840898    44840898    0,0,0   2   114,78  0,2378  26  circRNA H2AZ2   NM_138635 3,2   chr7:44835658-44840898|chr7:44843354-44847968
chr18   49491282    49491347    circular_RNA/1  1   -   49491282    49491282    0,0,0   1   65  0   1   circRNA SNORD58A    NR_002571   1   None|None
chr6    31835262    31835326    circular_RNA/8  0   +   31835262    31835262    0,0,0   1   64  0   8   circRNA SNORD48 NR_002745 None|None
chr6    143474856   143479052   circular_RNA/16 0   +   143474856   143474856   0,0,0   1   4196    0   16  ciRNA   PEX3    NM_003630 chr6:143474856-143479075
chr1    44775864    44775938    circular_RNA/16 1   +   44775864    44775864    0,0,0   1   74  0   16  circRNA SNORD55 NR_000015 None|None
chr1    164563311   164641005   circular_RNA/12 0   +   164563311   164563311   0,0,0   1   77694   0   12  ciRNA   PBX1    NM_002585 chr1:164563311-164792493
chr1    173864368   173864445   circular_RNA/11 1   -   173864368   173864368   0,0,0   1   77  0   11  circRNA SNORD47 NR_002746 None|None
chr1    173865967   173866028   circular_RNA/2  0   -   173865967   173865967   0,0,0   1   61  0   2   circRNA SNORD44 NR_002750 None|None
chr1    202010706   202011097   circular_RNA/7  1   +   202010706   202010706   0,0,0   1   391 0   7   ciRNA   ELF3    NM_004433 chr1:202010706-202011128
chr3    49100695    49101354    circular_RNA/8  0   -   49100695    49100695    0,0,0   1   659 0   8   ciRNA   QARS1   NM_001272073    10  chr3:49100674-49101354
chr17   81704430    81704611    circular_RNA/2  1   +   81704430    81704430    0,0,0   1   181 0   2   ciRNA   MRPL12  NM_002949 chr17:81704430-81704632
chr19   7606571 7607798 circular_RNA/1  1   +   7606571 7606571 0,0,0   1   1227    0   1   ciRNA   CAMSAP3 NM_020902   4   chr19:7606571-7608125
chr19   49490906    49490972    circular_RNA/2  1   +   49490906    49490906    0,0,0   1   66  0   2   circRNA SNORD34 NR_000019 None|None

By the way:

The last two rows of file C190476.Chimeric.out.junction are somthing like below, the last second row will raise an Exception when parsing the file, thus I removed the last second row manually and the 'parse' command goes well. I hope I did not make a mistake.

# 2.7.0f   /nfs2/software/STAR-2.7.0f/bin/Linux_x86_64/STAR....... --chimOutType Junctions
# Nreads 48628025   NreadsUnique 39251472   NreadsMulti 6787857

[kepbod]

Thanks for your feedback. Could you offer the version of STAR you use? STAR may update some parameters leading to these bizarre results. I will check to make CIRCexplorer to be compatible to the updated STAR.

[gudeqing]

hi, @kepbod
STAR-2.7.0f/bin/Linux_x86_64/STAR was used

[kepbod]

Sorry for the late reply. The first line in your results is ciRNA, aka circular intronic RNA. It is not the circRNA from back-splicing of exons. For the commented lines, they are derived from the option "chimOutJunctionFormat" in STAR, and the default setting is off, so we did not take care of it.