weir12
commented
1 year ago Hi,
Thank you for expressing interest in our project. I believe this issue may be attributed to a problem with tombo. Perhaps we should seek assistance from @marcus1487 to resolve it, or have you examined the success rate of alignment using minimap2 alignment on transcriptome files? This factor greatly influences and contributes to the occurrence of Alignment not produced
Best wishes,
Liang
Dear DENA author,
I have a potential issue when I run the tombo re-sqguiggle step, I lost around half of my reads that cannot pass the re-sqguiggle step. Is that expected? Did you face to this issue? Do you have an idea what could be the cause. I am using the same transcriptome of Arabidopsis you used.
I already checked potential solution on Tombo "issue" but found no solution/explaination.
I got something like that below:
100%|▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒▒| 2977277/2977277 [14:30:45<00:00, 56.99it/s] [07:12:26] Final unsuccessful reads summary (49.4% reads unsuccessfully processed; 1470935 total reads): 47.8% (1422467 reads) : Alignment not produced 1.6% ( 46193 reads) : Poor raw to expected signal matching (revert with
tombo filter clear_filters) 0.1% ( 2264 reads) : Read event to sequence alignment extends beyond bandwidth 0.0% ( 7 reads) : Reference mapping contains non-canonical bases (transcriptome reference cannot contain U bases) 0.0% ( 2 reads) : Not enough raw signal around potential genomic deletion(s) 0.0% ( 2 reads) : Fastq slot not present in --basecall-groupOtherwise all the steps from your tool DENA works perfectly!
Hope you can help me for that.