Other AS types counting, no output

[zhaoshuoxp]

Hi Yuanhua,

I am using v2.2 to count other types of AS, A3SS for example:

brie-count -a ~/genome/mm10/mouseAS/A3SS.gff3 -o . -S bamfile.list -p 8 -t Any

Even with -t Any option, this command still gives error message and stuck like forever:

[BRIE2] example head cells:
[['/..../116434_42_3.bam'
'116434_42_3']
['/..../116434_61_39.bam'
'116434_61_39']
['/..../116434_8_46.bam'
'116434_8_46']] ...
[BRIE2] loading gene annotations ... Done.
[BRIE2] counting reads for 6104 genes in 3140 sam files with 8 cores...
This is not exon-skipping event!
None
This is not exon-skipping event!
None
This is not exon-skipping event!
None

Did I miss anything or put something wrong?

Many thanks!

Quanyi

[liuyu988]

Hi Quanyi，
Have you sovled this problem?i seem to meet the problem similar to yours. thanks!

LiuYu

[zhaoshuoxp]

Hi Quanyi， Have you sovled this problem?i seem to meet the problem similar to yours. thanks!

LiuYu

Not yet.

[huangyh09]

Thanks both for trying out the new feature on other splicing types. Sorry it's actually a minor bug in the code, as we only tested the other splicing events in droplet data.

Now, it has been fixed to support smart-seq in the new release v2.2.1. Please upgrade your package, e.g., by pip install -U brie and try your command line again.

Yuanhua

[liuyu988]

Thanks both for trying out the new feature on other splicing types. Sorry it's actually a minor bug in the code, as we only tested the other splicing events in droplet data.

Now, it has been fixed to support smart-seq in the new release v2.2.1. Please upgrade your package, e.g., by pip install -U brie and try your command line again.

Yuanhua

Thank you for your reply! Yu

[TuoCai2000]

Hi Quanyi,
I notice that you use the command brie-count with annotation '/genome/mm10/mouseAS/A3SS.gff3' , can you tell me how to generate it? like intron retension and A3SS.etc
Thank you!

Tuo

[zhaoshuoxp]

Hi Quanyi, I notice that you use the command brie-count with annotation '/genome/mm10/mouseAS/A3SS.gff3' , can you tell me how to generate it? like intron retension and A3SS.etc Thank you!

Tuo

HI Tuo, I simply use the briekit (https://github.com/huangyh09/briekit/wiki) to generate them from GENCODE GTF file. Please note that the filtering function of it does not work on my end so I just use the unfiltered GFF to proceed.
Quanyi