No annotated items in example case

[ntbeileh]

I am running through the example use case for annotation and none of the RNAs are getting annotated.

This is the command I am using: COMPSRA % java -jar COMPSRA.jar -ref hg38 -ann -ac 1,2,3,4,5,6 -in ./example_out/sample01/sample01_17to50_FitRead_STAR_Aligned.out.bam -out ./example_out/sample01/sample01_17to50_FitRead_STAR_Aligned

And this is the output I am getting:
[miRBase]
Total Annotation Items: 4694
Annotated Items (covered by least one read): 0
Unannotated Items: 4694
Reads Support the Annotation: 0

{piRNA}:
[piRNABank]
Total Annotation Items: 665175
Annotated Items (covered by least one read): 0
Unannotated Items: 665175
Reads Support the Annotation: 0
[piRBase]
Total Annotation Items: 804849
Annotated Items (covered by least one read): 0
Unannotated Items: 804849
Reads Support the Annotation: 0

{tRNA}:
[GtRNAdb]
Total Annotation Items: 601
Annotated Items (covered by least one read): 0
Unannotated Items: 601
Reads Support the Annotation: 0

{snoRNA}:
[GEN_snoRNA]
Total Annotation Items: 1006
Annotated Items (covered by least one read): 0
Unannotated Items: 1006
Reads Support the Annotation: 0

{snRNA}:
[GEN_snRNA]
Total Annotation Items: 2053
Annotated Items (covered by least one read): 0
Unannotated Items: 2053
Reads Support the Annotation: 0

{circRNA}:
[circRNA]
Total Annotation Items: 140195
Annotated Items (covered by least one read): 0
Unannotated Items: 140195
Reads Support the Annotation: 0

I am not sure what is going wrong here. Any help is appreciated!

[cougarlj]

Dear ntbeileh, In such a situation, I will check the QC part. Please check the QC report and make sure the distribution of miRNA length is right. Best regards, Jiang Li

…

On Sat, Apr 9, 2022 at 7:33 AM ntbeileh ***@***.***> wrote: I am running through the example use case for annotation and none of the RNAs are getting annotated. This is the command I am using: COMPSRA % java -jar COMPSRA.jar -ref hg38 -ann -ac 1,2,3,4,5,6 -in ./example_out/sample01/sample01_17to50_FitRead_STAR_Aligned.out.bam -out ./example_out/sample01/sample01_17to50_FitRead_STAR_Aligned And this is the output I am getting: [miRBase] Total Annotation Items: 4694 Annotated Items (covered by least one read): 0 Unannotated Items: 4694 Reads Support the Annotation: 0 {piRNA}: [piRNABank] Total Annotation Items: 665175 Annotated Items (covered by least one read): 0 Unannotated Items: 665175 Reads Support the Annotation: 0 [piRBase] Total Annotation Items: 804849 Annotated Items (covered by least one read): 0 Unannotated Items: 804849 Reads Support the Annotation: 0 {tRNA}: [GtRNAdb] Total Annotation Items: 601 Annotated Items (covered by least one read): 0 Unannotated Items: 601 Reads Support the Annotation: 0 {snoRNA}: [GEN_snoRNA] Total Annotation Items: 1006 Annotated Items (covered by least one read): 0 Unannotated Items: 1006 Reads Support the Annotation: 0 {snRNA}: [GEN_snRNA] Total Annotation Items: 2053 Annotated Items (covered by least one read): 0 Unannotated Items: 2053 Reads Support the Annotation: 0 {circRNA}: [circRNA] Total Annotation Items: 140195 Annotated Items (covered by least one read): 0 Unannotated Items: 140195 Reads Support the Annotation: 0 I am not sure what is going wrong here. Any help is appreciated! — Reply to this email directly, view it on GitHub <#36>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABGMAD6EPIUPATU37SQCN7LVEC65ZANCNFSM5S54IERA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[ntbeileh]

Here is the QC report for the example use case:
sample01_QCReport.txt

There is a really high number of reads with zero length. However this is the example data and I've been just following the test examples. Still not sure why it is not annotating.

Best,

[cougarlj]

Dear ntbeileh, Please check the quality of samples. Also, it seems there are lots of short breaks of RNAs inside. Best regards, Jiang Li

…

On Wed, Apr 13, 2022 at 3:39 AM ntbeileh ***@***.***> wrote: Here is the QC report for the example use case: sample01_QCReport.txt <https://github.com/cougarlj/COMPSRA/files/8467626/sample01_QCReport.txt> There is a really high number of reads with zero length. However this is the example data and I've been just following the test examples. Still not sure why it is not annotating. Best, — Reply to this email directly, view it on GitHub <#36 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABGMAD57PY3BZEETXY3LPV3VEXGO7ANCNFSM5S54IERA> . You are receiving this because you commented.Message ID: ***@***.***>

[ntbeileh]

Hi Jiang,

These files are from the provided example dataset in this repository. I was going through the example use case as defined in the README in section 3.2 Test Examples. Shouldn't they be annotating as is?

Thanks

[omarbashth]

Hi Jiang,

I am facing a similar issue as the above with the example provided in the repository. Any idea what the issue might be.

Regards,
Omar