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WGLab / NanoRepeat

NanoRepeat: fast and accurate analysis of Short Tandem Repeats (STRs) from Oxford Nanopore sequencing data
MIT License
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No expectation output #15

Closed HLHsieh closed 4 months ago

HLHsieh commented 4 months ago

Hi Li,

I have used v1.4 for a long time, but some samples took a really long time to process. Therefore, I decided to try the new --fast-mode flag in the latest version. I tested it on a sample that was successfully analyzed in v1.4. However, I did not get the expected output as I did from the previous version.

The summary report from v1.4:

Summary_file=C9ORF72.chr9-27573528-27573546-GGCCCC.summary.txt  Repeat_Region=chr9-27573528-27573546-GGCCCC Method=GMM  Num_Alleles=1   Num_Removed_Reads=0 Allele1_Num_Reads=4 Allele1_Repeat_Size=16

The output.tsv from v1.8:

chr9    27573528    27573546    GGCCCC  0   -1  -1  Allele_Repeat_Size;Allele_Num_Support_Reads Read_Name;Read_Repeat_Size;Read_Allele_ID;PhasingConfidence

Additionally, the details folder only contained a chr9 subfolder without any files inside it.

Any suggestions would be appreciated.

Best, Hsin-Lun

fangli80 commented 4 months ago

This is because your input is FASTA but not FASTQ. The v1.8 version has a bug that cannot process FASTA, which is fixed now. Please clone the latest version.

HLHsieh commented 4 months ago

Thank you. The issued was fixed.

kaichop commented 4 months ago

Thank you for letting us know. Close it now.