Closed sid5427 closed 3 years ago
Hi,
I would try to install in a clean base environment. Necklace will also try to install conda itself and who know what sort of issues that might cause. If that fails, you could try editing the tools.groovy file manually to point to your installed packages like you suggest.
For your other questions:
Yes that's right. Alternatively you can leave the "-p de_novo_assembly_file=
Sorry, I think the documentation is a bit old. Necklace now takes a fasta file of protein sequences from a related species instead of a genome and annotation. So to use multiple related species just cat them all together. e.g.:
cat species1.fasta species2.fasta species3.fasta > related_species.fasta
and then use
proteins_related_species="
Cheers, Nadia.
Hi Nadia,
Thank you for your previous help - the pipeline worked well and we have been able to generate a supertranscript assembly of our rna-seq samples with some potential new genes.
We are in the process of writing up our work and I was wondering if you could explain a bit more on how exactly is the related species protein fasta file being used as opposed to related genome as described in the Necklace paper. I assume the protein sequences are being aligned to a consensus sequence which is generated from a cluster of similar transcripts from denovo and genome guided assembly?
Thanks for your help!
Hi, I'm so glad you've found Necklace useful in your data analysis!
The protein sequences from related species are used in a fairly similar way as how we described in the original paper. Rather than clustering first and then aligning, Necklace uses the alignment results to cluster. These are the steps in the clustering:
I hope this sort of makes sense and of course there is quite a bit of detail I've left out that I'd be happy to expand on if you need.
Cheers, Nadia.
Hi,
I downloaded necklace and tried the installation steps. The installation completed successfully but reported that it could not find or install hisat2, stringtie and samtools. I suspect this might be because I was running within a conda environment where I have various bioinformatics tools installed including the 3 above.
Should I just try a separate installation for necklace from "base" environment - i.e. no conda environment active? or edit tools.groovy to point to the path of the tools installed within conda.
Along with the above question - I have two more small queries -
I already have a trinity denovo assembled transcriptome in fasta format and I can pass it to necklace using -p de_novo_assembly_file= option. I am assuming I still have to format the config file as suggested? no special changes needed to it?
Is there anyway I could try using more than one related species' genome and annotation? or am I limited to one?