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Hello,
I am trying to predict the longest ORF using transcoder on the assembled transcript from public database.
I used following code:
TransDecoder.LongOrfs -t {directory}/GINQ01000001.fastq
…
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Hi, there
These day I have asked so many quesion about the PASA and say sorry for it. I have used the BUSCO to evaluate the cds.fa file from the PB data and the BUSCO was 91%. I wan to use the PA…
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Hi,
I'm getting an error 2304 with gmap.
My command is:
/global/group/home/harrisom/Programs/PASApipeline/Launch_PASA_pipeline.pl -c /global/group/home/harrisom/Programs/PASApipeline/pasa_conf/conf…
MCH74 updated
3 years ago
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I've clone the lastest PASA version, but when trying to use the perl script
`perl /home/buitracn/Genomes/Genome.tools/PASApipeline/Launch_PASA_pipeline.pl` I get that issue. Are their instruction o…
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Hello all,
I'm running TransDecoder.LongOrfs on a transcriptome using the following command line:
nohup TransDecoder.LongOrfs -t /media/raid/transcriptomes/data/trinityOUT/Trinity.fasta --gene_t…
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- [x] Add [get_accession](https://github.com/lifebit-ai/rmats-nf/blob/master/main.nf#L93-L117) process to download data from TCGA/GTEX
- [x] Extract FASTQ from BAMs using [bamtofastq](https://bedtool…
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Caused by: java.lang.RuntimeException: Cannot determine primaryIdentifier from GFF record:
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Caused by: java.lang.RuntimeException: Cannot determine primaryIdentifier from GFF record:
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Hi Brian,
I am seeing internal stop codons in many protein sequences generated after running TransDecoder.Predict and wondering what's causing the issue. I ran running LongOrfs first and then Pre…
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I am running the PASA assembly pipeline on a small input (~150kb), like this:
```
Launch_PASA_pipeline.pl -c alignAssembly.config -C -R -g Pt.fa -t transcripts.fasta --ALIGNERS blat
--TRANSDECODER …