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Hello!
Great project.
It appeared to be interesting for me to ask your opinion on current ORF reconstruction tools. You have chosen the Transdecoder. Are there shortcomings that are expected to appe…
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hello,
I want to ask about the final output file 'transcripts. Fasta. Transdecoder. Gff3' and 'transcripts. Fasta. Transdecoder. Genome. Gff3' what is the difference? I am using it for gene structure…
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Hi Brian,
I am using EVidenceModeler to combine different evidence and to have a final genome annotation.
I would like to include in my weight file:
- Ab initio gene prediction obtained from Au…
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Hi, there.
I have used the EVM model to combine lots of data to the annotation of a genome. I checked some results from the EVM results with the IGV. As shown in the picture, I confused about the…
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Hi,
I am trying to use the pipeline on an already assembled transcriptome (a single FASTA file with ~300k sequences) which I am putting in a directory called `onlyAnn` as per the instructions. I be…
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I think it might make sense to replace kallisto with this tool: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-021-08278-7
We could reduce the size of the proteome predicted by transde…
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Dear Brian,
We are trying to create the best ORF prediction for each transcript in a fasta file.
We run TransDecoder.LongOrfs with the --complete_orfs_only flag.
Then run TransDecoder.Predict w…
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HI, i am new here..
I followed tutorial and I wrote my pipeline below.
1. Assemble with Trinity tool
2. estimate abundance and normalize with RSEM
and with isoform matrix, I run DEG analysis…
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I made the exons and splice-sites files. However, the splice-sites file was empty so I excluded it. I got the same error when including the splice-site file too tho.
Any thoughts?
Command:
…
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Hi,
Thanks for the useful tool.
I am currently uncertain about the optimal type of transcriptome files to provide for my study. I am considering two approaches: directly using StringTie/Trinity fo…