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code:
cut -f 1 -d ' ' ./SQANTI3_1_output/muscle_corrected.fasta > ./SQANTI3_1_output/cdna.new.fa
grep '^>' ./SQANTI3_1_output/cdna.new.fa | cut -d ' ' -f 1 | sed 's/^>//g' > /home/D…
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Hi, I ran PASA with singularity to perform transcripts assembly and annotation update. The alignment assembly step ran successfully, but the update step ran with error, here are the error information:…
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### Suggestion Description
As new instructions/features are added with each new arch, it is useful to know the target architecture at compile time to employ separate code paths. For example: FP64 M…
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Hi,
I am new to SNV calling and I was wondering if it makes sense to use longshot on nanopore direct cDNA data. I was also wondering if the tool can be used to perform isoform-level phasing.
Tha…
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Hi,
I tried to upload a rice cDNA FASTA file for reference, but failed with an error code below:
"Starting job.
Error: ErrorException: rename(/rnadetector/ws/storage/app/public/jobs/6//rnadete…
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Hi Alex,
I observed a phenonome when I run the new release function _Barcode and cDNA on the same mate_. You give us an example to set the readFilesIn. reads1 fastq is at the first palce and the re…
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Hello there,
I hope you're having an awesome day, and that all is going well on our side. I just wanted to reach out to you because I ran into an issue when installing/building cDNA_cupcake using t…
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Hello, everyone
I used the PASA (v2.5.3) pipeline to update the annotations from EVM with the following command: `/vol2/YL_group/YL/software/PASApipeline-master/Launch_PASA_pipeline.pl -c alignAssemb…
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Feedback from Wednesday, July 10 meeting.
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Currently, we assume NM_007294.3 and NM_000059.3 for cdna coordinates coming from gnomad (see https://github.com/BRCAChallenge/brca-exchange/blob/master/pipeline/gnomad/gnomad_to_vcf.py#L103-L106). Is…