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gymrek-lab / LongTR

Tandem repeat genotyping with long reads
GNU General Public License v2.0
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Low base quality score for ONTs data #4

Closed quantrannnn closed 6 months ago

quantrannnn commented 6 months ago

Hello, I tried running LongTR for my ONT datas but the output filters out most of my reads because of the low base quality score: 181 reads overlapped region, of which: 5 were hard clipped 0 had an 'N' base call 176 had low base quality scores 0 did not have a unique mapping 0 PASSED ALL FILTERS I alreadly set --min-sum-qual to 0 or 7. This dataset worked with STraglr and TRGT. Could you help me? Thanks,

heliziii commented 6 months ago

Hello,

Thank you for using LongTR! Can you please pull and install the latest version? --min-sum-qual is now changed to --min-mean-qual with the default value of 30, showing the average quality score over the sequence.

Please let me know if you have any other questions.

Best, Helia

quantrannnn commented 6 months ago

Hi Helia,

Thank you! I installed the latest version and it works well now.

Best,

heliziii commented 6 months ago

Great!