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index error #919
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Looks like you are using should instead be such that the decoy sequences occur last. |
The ~/data/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa is genome, the ./SQANTI3_1_output/cdna.new.fa is trans, therefore I don't know where is error. |
You specify in the |
code:
cut -f 1 -d ' ' ./SQANTI3_1_output/muscle_corrected.fasta > ./SQANTI3_1_output/cdna.new.fa
grep '^>' ./SQANTI3_1_output/cdna.new.fa | cut -d ' ' -f 1 | sed 's/^>//g' > /home/Dingzifeng/SQANTI3_1_output/cdna.decoys.txt
cat ./SQANTI3_1_output/cdna.new.fa ~/data/Sus_scrofa.Sscrofa11.1.dna.toplevel.fa > ./trans_genome.fa
singularity exec /home/Singusoft/miniconda3_bedtools_mashmap_salmon.simg salmon index -t /home/Dingzifeng/SQANTI3_1_output/trans_genome.fa -d /home/Dingzifeng/SQANTI3_1_output/cdna.decoys.txt -i ~/salmon_index
result:
[2024-03-18 23:23:14.069] [puff::index::jointLog] [critical] Observed a non-decoy sequence [1] after having already observed a decoy. However, it is required that any decoy target records appear, consecutively, at the end of the input fasta file. Please re-format your input file so that all decoy records appear contiguously at the end of the file, after all valid (non-decoy) records
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