SalmonTools
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COMBINE-lab
Useful tools for working with Salmon output
The job getw killed when it truis to index the masked genome. Do you have any clue on how much ram this process consumes. I only have 8 gigs of...
Hi, I am running generatedecoytranscriptome.sh. But this step seems very time-consuming, so I submitted to slurm for execution. How long does it take to finish it? I applied for 1...
Hi, I have a GFP and transposon sequence which I want to incorporate for RNASeq analysis. I tried doing this with STAR, but it gives me only the TE sequence...
I'd like to include this in one of our pipelines, can you tag a release for SalmonTools? I'll add it to Bioconda then :)
Hi all, I get `Segmentation fault (core dumped)` on step 3 of `generateDecoyTranscriptome.sh`. I've filed https://github.com/marbl/MashMap/issues/21 upstream with more detailed information. I wanted to file an issue here in case...
Hi I'm stuck at the moment to generate a decoy file from two transcriptome fasta files (A. thaliana cDna and ncrna from Ensemblplants). I tried several ways of putting both...
I've made a docker container for SalmonTools https://quay.io/repository/comp-bio-aging/salmon-tools However, I constantly get: /opt/SalmonTools/scripts/generateDecoyTranscriptome.sh: line 105: 21 Killed $mashmap -r reference.masked.genome.fa -q $txpfile -t $threads --pi 80 -s 500 I run...
Perhaps you can shed some light on top this - very occasionally, we see salmontools processes which seem to never terminate. Here you can see some which have been operating...
Dear Authors, I tried to run the generateDecoyTranscriptome.sh script for the human genome. However, it couldn't complete step 3, which involves mashmap, due to a memory issue, despite using a...
