Hi, I’m new to RNA seq and I’m trying to use blastx on galaxy to blast a fasta file of possibly novel lncRNAs using the ncbi nr database. I want to remove transcripts with significant homology to known proteins with: e-value < 1e-10, target coverage > 80%, and identity > 90%, so I can preserve tran…

@gallardoalba I tried it with choose remote file option and it worked perfectly

Hi @bart_joosten , could you describe to me your pipeline until now? Do you have raw RNA-seq data or assembled transcripts? Which species do the samples correspond to? Regards

In addition to @gallardoalba 's question - yes, runtime can be substantial for this tool and will depend on how many input sequences you’re trying to match against the database. This is simply how it is. Regarding your identity threshold: % identity is part of the output you’re getting? If so, you…

I can also add my two cents. As already mentioned it is expected that it takes long. The ncbi nt and nr database are growing insanely fast. If I need to blast a large amount of sequences I always make a subselection first. So I only blast against homo sapien sequences for example. But this may be no…

@gallardoalba Hi, thanks for your reply. I’m trying to find novel lncRNAs. I have used fastq files from human samples and performed trimming (trimmomatic), alignment (hisat2), assembly (stringtie) and have used the merged assembled files (stringtie-merge) in the FEELnc package to find potential new …

@gbbio I like your suggestion of using the diamond tool! It has all the parameters that I want to use on blastx and should perform faster. I’m trying it right now on galaxy.

@gbbio I have tried using diamond and it works well. However the diamond output in default outputs matching protein transcripts from all taxi but I am of course only interested in human transcripts but I’m having some problems selecting the human taxon id in the diamond tool. Entering the human taxo…

Hi @bart_joosten , I tried to upload the file, and I didn’t find any problem history . How did you try to upload it? Regards

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