Fastq downloaded from SRA showing error at identify off-targets step

[asgarhussain]

I am able to align fastq file from SRA successfully. But I am getting following error at off-target step

[08/06 12:11:40PM][INFO][guideseq] Identifying offtarget sites...
[08/06 12:11:40PM][INFO][identifyOfftargetSites] Processing SAM file output1/aln1/aligned/SRR1695633_r1.sam
[08/06 12:11:40PM][ERROR][guideseq] Error identifying offtarget sites.
[08/06 12:11:40PM][ERROR][guideseq] Traceback (most recent call last):
File "guideseq/guideseq.py", line 231, in identifyOfftargetSites
identifyOfftargetSites.analyze(samfile, self.reference_genome, self.identified[sample], annotations)
File "/home/asgar/asgar_work/dac/guideseq/guideseq/identifyOfftargetSites.py", line 217, in analyze
chromosome_position.addPositionBarcode(chromosome, read_position, strand, barcode, primer, count)
File "/home/asgar/asgar_work/dac/guideseq/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'

Does script not support the fastq file without bar code information ?

[madaojjc]

Hi, I met the same issue, have you ever solved it? THANKS

[asgar-hussain]

@madaojjc They have not provided the bar code file in the SRA. I think off-target step can not run without it.

[wenhuihuang1979]

@asgar-hussain why? if not, how can we repeat their results?

[Bathroomboss]

The same question to you. Can we get the "index reads" from SRA and repeat their results?