I am having this problem using the SAM file to identify the off-target
$python /home/data/vip55/software/guideseq-master/guideseq/guideseq.py identify --aligned G2-1_S3_L004_R1_001.sam --genome /home/data/vip55/index/hg38/GRCh38.p13.genome.fa --outfolder ~/1work/guide-seq/L1-1-G4-2-0.5lane --target_sequence AGCCCCAGCAAGAGCACAAGAGG --description G2-1_S3_L004_R1_001
[09/26 05:23:50PM][INFO][guideseq] Identifying offtarget sites... [09/26 05:23:50PM][INFO][identifyOfftargetSites] Processing SAM file G2-1_S3_L004_R1_001.sam [09/26 05:23:50PM][ERROR][guideseq] Error identifying offtarget sites. [09/26 05:23:50PM][ERROR][guideseq] Traceback (most recent call last): File "/home/data/vip55/software/guideseq-master/guideseq/guideseq.py", line 222, in identifyOfftargetSites identifyOfftargetSites.analyze(samfile, self.reference_genome, self.identified[sample], annotations) File "/home/data/vip55/software/guideseq-master/guideseq/identifyOfftargetSites.py", line 217, in analyze chromosome_position.addPositionBarcode(chromosome, read_position, strand, barcode, primer, count) File "/home/data/vip55/software/guideseq-master/guideseq/identifyOfftargetSites.py", line 66, in addPositionBarcode self.chromosome_barcode_dict[chromosome][position][strand][barcode] += count TypeError: unsupported operand type(s) for +=: 'int' and 'NoneType'
Do you know what can be the problem? I did not use the UMI and started from "align" step
Thanks a lot for youtr time
