Alternative to Gentrome?
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12 weeks ago
yee • 0

For context, after running the salmon index line, the process is killed after clipping some poly-A tails. However, I don't have access to a higher computer, and I currently run on my ASUS G14 with 16.0 GB RAM, and 500gb of hard drive space.

salmon index -t gentrome.fa.gz -i IndexSalmonDecoyAware --decoys decoys.txt -k 7 --gencode

[2023-12-08 10:22:09.886] [puff::index::jointLog] [info] Replaced 151122967 non-ATCG nucleotides
[2023-12-08 10:22:09.886] [puff::index::jointLog] [info] Clipped poly-A tails from 2033 transcripts
Killed

Any thoughts on running on an alternative index, I initially generated a python script as a decoy and concatenated it and used it through the salmon index process. Which did work I suppose, but I'm not sure if its good to do so that way? Sorry, I'm new to bioinformatics.

salmon • 377 views
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Curious as to what is gentrome? Genome decoy + transcriptome?

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Could be either a hard-masked reference genome sequence or the decoy reference genome + transcriptome. If it's the latter (which takes much more memory to build the index), the OP could try the former using the helper script from salmon: https://github.com/COMBINE-lab/SalmonTools/blob/master/scripts/generateDecoyTranscriptome.sh

OP could also try the --sparse option while building the index:

  --sparse                      Build the index using a sparse sampling of 
                                k-mer positions This will require less memory 
                                (especially during quantification), but will 
                                take longer to construct and can slow down 
                                mapping / alignment
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