Error in CIRI2 as a circular RNA extracting tool for my data set

Question

[modarzi]

Hi,

My data set belong to 3 human that have cancer. I trimmed these samples and then align them with BWA MEM. Now, I use SAM file of my one sample(sra_data_SRR_1427482) for exacting its Circular RNA via CIRI2 tool based on below command:

perl CIRI2.pl -I sra_data_SRR_1427482.sam -O outfile -F chr1.fa -A chr1.gtf

but I recieve below message:

i May 18 18:43:04 2018] CIRI begins running [Fri May 18 18:43:04 2018] Loading reference

The following chromosomes are not found in chr1.fa: chrUn_gl000237 chrUn_gl000234 chr19_gl000208_random chrUn_gl000215 chr2 chrUn_gl000225 chrUn_gl000236 chr1_gl000192_random chrUn_gl000232 chr20 chrUn_gl000226 chr17_gl000204_random chr12 chr4_gl000194_random chrUn_gl000245 chr18_gl000207_random chr17_gl000203_random chr5 chrUn_gl000241 chrUn_gl000229 chrUn_gl000239 chr9_gl000198_random chrUn_gl000242 chrUn_gl000224 chrUn_gl000223 chr8 chrUn_gl000219 chr11_gl000202_random chrUn_gl000248 chr16 chr3 chrUn_gl000214 chr21 chrUn_gl000246 chrUn_gl000231 chr13 chr17 chr9_gl000201_random chr21_gl000210_random chr4_ctg9_hap1 chr22 chr7 chrUn_gl000243 chr9 chr18 chrUn_gl000247 chr19_gl000209_random chrUn_gl000228 chr7_gl000195_random chrY chr8_gl000197_random chr17_ctg5_hap1 chrUn_gl000238 chrUn_gl000249 chr4_gl000193_random chr6_qbl_hap6 chr19 chr14 chrUn_gl000221 chr8_gl000196_random chrUn_gl000217 chrUn_gl000212 chr17_gl000205_random chrUn_gl000222 chr6_dbb_hap3 chr6_ssto_hap7 chrUn_gl000218 chrUn_gl000244 chr6_apd_hap1 chr11 chr15 chr4 chrUn_gl000235 chrUn_gl000213 chr9_gl000199_random chrUn_gl000211 chr6 chrUn_gl000230 chr6_mcf_hap5 chrUn_gl000240 chr6_cox_hap2 chr10 chrUn_gl000233 chr6_mann_hap4 chrUn_gl000216 chrUn_gl000227 chrUn_gl000220 chr1_gl000191_random chr9_gl000200_random chr17_gl000206_random chrX Fatal error. Aborted.

I don't know what is my problem for running CIRI2. because I ran test_data2.zip perfectly and withput error.

My data set is Single-End and CIRI2 is stand for CircRNA Identifier. A de novo circular RNA identification tool.

I appreciate if anybody share his/her comment with me.

Best Regards, Mohammad

Answer 1

[Grouse]

From what you've provided I recommend running CIRI with a complete human reference sequence (the same used in bwa) and with a complete annotation file.

It looks like CIRI is trying to look for reference chromosomes which are not there.

Answer 2

[archana.bioinfo87]

Dear,

I think you should try with whole genome fasta file and respective annotation file in gtf format. Hope it will work. Something like this

perl CIRI2.pl -I test1_rawaln-pe.sam -O test1_raw_ciri_outfile -F hg19_genome.fa -A gencode.v17.annotation.gtf