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According to RefSeq (NM_003283),
This gene encodes a protein that is a subunit of troponin, which is a regulatory complex located on the thin filament of the sarcomere. This complex regulates striated muscle contraction in response to fluctuations in intracellular calcium concentration.
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$> astalavista -t astafunk --tref --gtf tnnt1.gtf --genome ~/example/genome/ > reference_tx.fasta |
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$> hmmsearch --domtblout reference_file ~/Databases/Pfam/Pfam-A.hmm reference_tx.fasta |
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or skip these commands and use directly the whole database Pfam-A.hmm as parameter for the option [–hmm]. |
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astalavista -t astafunk --genome ~/example/genome/ --gtf tnnt1.gtf --reference reference_file --hmm database.hmm |
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Description of the output columns can be found in 3.4 - Tool ASTAFUNK (Prediction of functional domains impacted by AS).
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Convert our output to BED track:codecat output | awk -v FS="\t" -v OFS="\t" 'NR>1{split($1,chr,"chr"); if($9<0){s1 = $9*(-1);s2=$8*(-1);st="-"}else{s1=$8;s2=$9;st="+"}print $1, s1-1,s2, $3"-"$4, $5*100,st}'