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a-slide / NanoCount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2
https://a-slide.github.io/NanoCount/
MIT License
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Est_count doesn't match records #32

Closed KunFang93 closed 9 months ago

KunFang93 commented 9 months ago

Hi,

Thanks for providing this wonderful tool! I am a fresh user for NanoCount and this might be a silly question..: I have used the command NanoCount -i ../minimap2/gControl_trim_filt1k.sam -b gControl_trim_filt1k_selected.bam --extra_tx_info -o gControl_counts.tsv to run nanocount.

And I summed all est_count in gControl_counts.tsv file and got the total number of 455586, however, I checked gControl_trim_filt1k.sam and it has 5184460 mapped reads. I wondered why there are such big difference in term of number of reads?

Thanks in advance!

Best, Kun

KunFang93 commented 9 months ago

I double checked with my experiment labmate and found my data is from direct cDNA sequencing... sry for bothering...

josiegleeson commented 9 months ago

Hi Kun,

If you have cDNA data you can disable the 3' end filtering by using '-d -1' in the command. However, we haven't benchmarked this extensively.

Thanks, Josie.

KunFang93 commented 9 months ago

Sorry for late reply. Yes, I saw it in the manual~ thanks for providing this wonderful tool!