umitools dedup error: '<' not supported between instances of 'str' and 'bytes'
See original GitHub issueHi, thank you so much for offering this wonderful tool.
I’m trying to deduplicate single-cell RNA-seq bam files mapped by STAR. By reading this thread, I want to compare the results of
--umi-tag=UR --cell-tag=CR
and
--umi-tag=UB --cell-tag=CB --method=unique
The former works fine but the latter somehow gives the error as:
Traceback (most recent call last): File "/home/anaconda3/bin/umi_tools", line 11, in <module> sys.exit(main()) File "/home/anaconda3/lib/python3.8/site-packages/umi_tools/umi_tools.py", line 61, in main module.main(sys.argv) File "/home/anaconda3/lib/python3.8/site-packages/umi_tools/dedup.py", line 309, in main for bundle, key, status in bundle_iterator(inreads): File "/home/anaconda3/lib/python3.8/site-packages/umi_tools/sam_methods.py", line 488, in __call__ for k in sorted(self.reads_dict[p].keys()): TypeError: '<' not supported between instances of 'str' and 'bytes'
even if the rest of the codes are identical. I’m using umitools v.1.1.2 and the exact codes are as follows:
umi_tools dedup --per-cell -I Aligned.sortedByCoord.out.bam --extract-umi-method=tag --umi-tag=UB --cell-tag=CB --method=unique -S Aligned.sortedByCoord.out_deduplicated_UB_CB.bam
umi_tools dedup --per-cell -I Aligned.sortedByCoord.out.bam --extract-umi-method=tag --umi-tag=UR --cell-tag=CR -S Aligned.sortedByCoord.out_deduplicated_UR_CR.bam
Do you have any ideas where I missed? Thank you so much for your help.
Best, Raku
Issue Analytics
- State:
- Created a year ago
- Reactions:1
- Comments:5 (2 by maintainers)
Top GitHub Comments
@vivekbhr @TomSmithCGAT I’m so sorry for my late response. Somehow I did not receive the notice. It worked perfect once I filtered out the reads with CB:Z:-! Thank you so much for your help and I’m closing the issue.
Ah, brilliant. @camelest, does that solve your error too?