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Dear Brian Haas,
I am trying TransDecoder to get CDS from RNA-seq aligned to genome using Cufflinks. Since the assembly transcripts from RNA-seq may not be full-length CDS, I am wondering whether T…
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Hello,
I have isoseq data and my final transcripts are full length. Because, we chose the 5' cap linker selection method to make cDNAs. I am trying to improve the gene models and using PASA pipeline.…
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Hi, I am having persistent formatting issues when I use conversion utils? I am running transdecoder version 5.5.0.
I have a .gtf file generated from merging multiple Stringtie gtf files:
`> head …
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Hi there,
This is a semi-automated message from a fellow bioinformatician. Through a GitHub search, I found that the following source files make use of BLAST's `-max_target_seqs` parameter:
- [samp…
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the `check_program` function fails in some cases because the code checks for a `/` at the start of the path to the binary.
```
which cd-hit-est
~/.linuxbrew/bin/cd-hit-est
```
The reason for this is…
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Erica Lasek-Nesselquist
Dear Brian,
Is there anyway to specify other genetic codes than those listed? I'm specifically interested in NCBI's genetic code 29 (Mesodinium Nuclear)
https://www.…
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Dear Developers
I found that the genome GFF file made by Transdecoder were something wrong. when I extract the CDS, some of the CDS are different than the sequence in longest_orfs.cds . I follwed …
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Hi,
I am having difficulty performing a BLASTP. When using the script suggested on the home page I get the message:
Blast database error: no index file or alias for protein database [uniprot_s…
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May I integrate two blastp searches to predict the final orf? one of them using an NCBI database and the other one using the proteome of a related specie. May I pass two `--retain_blastp_hits`?
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Hello,
I'm trying to submit some mRNA sequences on NCBI. I used transdecoder to obtain the peptide sequences, and NCBI requests the CDS information.
My question is how can I determine if the read…