-
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.…
-
Hi,
I got many error sequences including many X after i used TransDecoder.LongOrfs. I don't know what went wrong.
> c69778_g1_i4.p2 type:internal len:176 gc:universal c69778_g1_i4:2-526(+)
XXXXXX…
-
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…
-
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…
-
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…
-
Hi @brianjohnhaas and company,
The lengths reported in the `TransDecoder` `FASTA` headers appear to be wildly off in some cases.
For example:
```
>TRINITY_DN24304_c0_g1_i1.p1 TRINITY_DN24304…
-
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`?
-
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.…
-
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 …
-
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…