Should circminer abort for bad reads?

[EricSHo]

Hi,

circminer detected there was a bad read in the fastq file (It's correct. I checked the fastq file) and aborted. Are there options I can set to bypass the abortion? It makes more sense to me to discard bad reads and move on.

Here's the error message:
ERROR: read: ST-E00167:388:HCKK2ALXX:3:2115:30472:38948, length of sequence (136) does not match with quality (127)!
Aborting

CircMiner 0.3.1

circminer --thread 3
--verbose 2
--gtf ../mm10/gencode.vM24.annotation.gtf
--reference ../mm10/GRCm38.primary_assembly.genome.fa
--seq1 ../fastq_dir/Mouse_F950-L${seqno}_good_1.fq.gz
--seq2 ../fastq_dir/Mouse_F950-L${seqno}_good_2.fq.gz
--output ${prefix}_circminer
--scan-lev 2
--rlen 150
--sam

Your help is appreciated.

Thanks again.

Eric.

[HosseinAsghari]

Hi,

This feature is not available in CircMiner at the moment. It's a good idea to add it in the next versions of the software. However, the best solution will be to use a quality control pipeline to remove the problematic reads from the input data and then feed it to CircMiner.