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Hello,
I used rnabloom to construct a transcriptome from direct RNA data with the following:
rnabloom -long all_reads.fastq -stranded -t 25 -outdir dir/ -u true
The rnabloom.transcripts.fa a…
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Hello,
Thanks for developing such a great tool. I am using IsoQuant to analyze ONT single-cell full-length transcriptome data and would like to obtain exon count information to calculate PSI. In th…
weib3 updated
1 month ago
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Dear Martin,
Thanks for developing this wonderful software for TE expression quantification. I have a question regarding the de novo transcriptome. For non-model organism, we could perform a de nov…
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After running Oxford nanopore direct RNA sequencing with total RNA as input, I preprocessed the data through fastp and then input the result for assembly with RNAbloom2 with the following command:
rn…
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### Operating System
Other Linux (please specify below)
### Other Linux
Red Hat Enterprise Linux release 8.6
### Workflow Version
v1.1.1-g999fb4e
### Workflow Execution
Command li…
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I'm trying to run Funannotate Predict with a genome (fasta), trinity assembly of transcriptome (fasta), and alignment (bam) input files.
I encounter the following error:
CMD ERROR: CodingQuarry -p…
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Hi,
Now I want to incorporate RNA-seq via PASA when conducting the genomic gene annotation. When I used the FastQC for assessing my Illumina RNA-seq data, I found there were many overrepresented seq…
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Good morning 😊
I am opening this issue on the recommendation of @rob-p and our discussion over on BioStar (https://www.biostars.org/p/486346/#486637).
I was using STAR to index and align my raw r…
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I have tried to download the binary for linux v1.0.3 but the link seems to be broken.
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Assemble RNAseq reads into a transcriptome assembly via Trinity or SOAP de-nova trans