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WGLab / LIQA

Long-read Isoform Quantification and Analysis
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could not find bam file #10

Closed Cristinex closed 6 months ago

Cristinex commented 3 years ago

It turned out to be error: .bam does not exist!

I run the command and the bam file in the same folder, it cannot find it. How to solve this problem?

Thank you!

huyustats commented 3 years ago

Please specify your bam file using option "-bam"

Cristinex commented 3 years ago

Here was my command.

liqa -task quantify -refgene <path>/xx.refgene -bam <path>/yy.bam -out <path>/output -max_distance 20 -f_weight 1

And I did not add any suffix for output since I did not know what format should be.

I did specified my bam file with -bam. Thank you for your reply!!!

huyustats commented 3 years ago

Please use "ls -l /yy.bam" to check it the file is there. Also, please sort and index the bam file before running LIQA. Thanks!

Cristinex commented 3 years ago

Thank you!! It work after indexing.

Another question, is it possible to use LIQA for hpv genome annotation? Since I downloaded hpv's gtf from https://www.ncbi.nlm.nih.gov/assembly/GCF_000863945.3/ and executed -task refgene. It turned out that 0 genes were processed. Was there any problem for this .gtf to be process?

agouru55 commented 6 months ago

Hi yes, I did the same and I was able to output processed genes. Perhaps as done above, sort/index the BAM before LIQA, and ensure you have the latest version of LIQA as you run the quantify task again.

This step also usually only outputs genes with 2 or more isoforms, which is why you may be running into this issue