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vpc-ccg / circminer

A sensitive and fast tool for circular RNA detection from RNA-Seq data
GNU General Public License v3.0
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Should circminer abort for bad reads? #3

Open EricSHo opened 4 years ago

EricSHo commented 4 years ago

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 commented 4 years ago

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.