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Hi,
We are trying to generate .tbl file for NCBI submission using convert_gff3_to_ncbi_tbl.py script at biocode. But the problem is, GFF3 produced by Transdecoder has multiple genes predicted for s…
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Hi,
I do not plan to use GeneMark-ET but I want to use Augustus, GlimmerHMM and SNAP.
1. If I ran `funannotate train` do I still have to use `funannotate predict --rna_bam `? If yes then what is …
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Hi,
I performed transdecoder on 13 RNA samples at first, and then included 18 more samples to perform gene prediction with transdecoder. Using the same genome( repeats unmasked), I was able to pred…
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HI,
> If you have RNA-Seq data and have reconstructed transcripts using a method such as [Cufflinks](http://cole-trapnell-lab.github.io/cufflinks/) or [PASA](http://pasapipeline.github.io/), you ca…
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I had this idea :
Youtube video subtitles are pure written form of human spoken words plus there are so many great videos out there , courses and content that is very precise in teaching and solvin…
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I'm not sure I really understand the goal of this tool.
From what i ran up to now, i have created a "clean" fastq file of the consensus transcripts from multiple clusters. I don't quite get how i …
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Hello,
Thank you so much for publishing this method! I'm excited to try it out on our data and have two questions.
First, how do you recommend handling missing data? Specifically, we work with l…
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Hi,
I used ./Trinity --seqType fq --left R1.fq.gz --right R2.fq.gz --max_memory 200G --CPU 128 --output ~/result/trinity in trinityrnaseq-v2.14.0 to run my data.
Inchworm showed /home/gcx/bio/tri…
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Greetings @brianjohnhaas,
I recently successfully completed trinity assembly (human breast cancer cell line MDA-MB-231). Using the output trinity .fasta file containing all the de novo transcripts,…
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Hi,
If there are several or many RNA samples, merge fastq files and then mapping and assemble OR mapping and assemble each sample separately?
Best,
Kun