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WGLab / LIQA

Long-read Isoform Quantification and Analysis
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Novel isoform detection #34

Closed AlinaO90 closed 3 months ago

AlinaO90 commented 1 year ago

Hello, the most recent download of this tool includes a function that is not written about here in the documentation:

liqa -task novel -ref <reference_file> -bamlist <list of bam file> -out <output_file>

What is the format for the -bamlist needed to run this function? I have tried the following

-bamlist mapped-BioSample1_filtered.bam [using the bam files filtered with samtools]

which results in error : "BAM file are invalid!"

and

-bamlist [mapped-BioSample1_filtered.bam, mapped-BioSample2_filtered.bam, mapped-BioSample3_filtered.bam]

which results in error : " does not exist!"

Thanks!

kaichop commented 11 months ago

@huyustats is this problem resolved?

huyustats commented 11 months ago

Hi @AlinaO90,

Please update LIQA to the newest version and follow the command of liqa -task novel. The input is bam file. Thanks!