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Hi @MichaelHiller and @kirilenkobm,
While inspecting TOGA results I found that some of the transcripts annotated had negative prediction scores:
`ENST00000373688 209092 -1.0`
This, in theory…
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To Whom It May Concern,
When trying to quantify isoform expression for a dataset (attached) by "**python $LIQA_PATH/LIQA.py -task quantify -refgene $refgene_PATH/chr1.refgene -bam $data_PATH/test1.…
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Hi,
The previous problem has been solved,but I encountered this error. raceback (most recent call last):
File "/public/home/jwtang/PacBio/FL_stickleback/ccs/FLNC/SQANTI3/sqanti3_qc.py", line 2537, i…
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Hi,
I want to compare the AS events identified from short reads with rmats to espresso long-read transcripts, so I can calculate that how many AS events can be verified by long reads, how can I ach…
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Hello,
I am working through the SQANTI-SIM tutorial and I encountered an error with the evaluation step.
######### Running the eval step
First I loaded the SQANTI-SIM conda environment:
**$ …
jkmh2 updated
11 months ago
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Hello!
I use long read RNA seq via the new branch “long-reads" to annotate a certain mammalian genome.
https://github.com/Gaius-Augustus/BRAKER/blob/master/docs/long_reads/long_read_protocol.md
W…
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A key requirement for finding an inhibitor of PLCz1 is to have an assay that will measure the activity of the protein against different compounds.
Previously used PLC activity assays use tritium l…
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**Operating system**
Linux
**Conda environment**
```
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
avro-python3 …
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Greetings,
My code for deduplicting my paired end data:
##Step-1:(barcode/umi extraction)**
```
umi_tools extract -I abc.fastq.gz --bc-pattern=CCCCCCCCNNNNN --read2-in=cba.fastq.gz --stdout=proc…
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Based on the work in #265 and #266 generate the glycan and protein schema. These schema files should be used in the automated testing to validate the glycan and protein details.
**Dependencies**:
…