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zhongzhd / ont_m6a_detection

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filter failed reads #12

Open AndreaYCT opened 7 months ago

AndreaYCT commented 7 months ago

Hi,

I'm trying to use your codes to run m6anet. During filter basecalling failed reads, i got some errors.

filter basecalling failed reads:

cd $wt_basecalled_fast5 mkdir workspace_fail awk '{if($10=="FALSE"){print $1}}' sequencing_summary.txt > fail_fast5.txt cat fail_fast5.txt | while read id;do mv workspace/$id workspace_fail;done

Later, i got some errors during nanopolish eventalign, how important is to filter failed reads?

Many thanks!

zhongzhd commented 5 months ago

So sorry for the late response; I couldn't log in to GitHub properly for a while. Regarding your question, failed reads indicate lower sequence reliability, so removing them should lead to more trustworthy results.