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aryeelab / guideseq

Analysis pipeline for the GUIDE-seq assay.
GNU Affero General Public License v3.0
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Fastq downloaded from SRA showing error at identify off-targets step #48

Open asgarhussain opened 5 years ago

asgarhussain commented 5 years ago

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 commented 4 years ago

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

asgar-hussain commented 4 years ago

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

wenhuihuang1979 commented 2 years ago

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

Bathroomboss commented 1 year ago

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