/scripts/01.1_commands-CDHIT-EST.txt
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# zagor
# set of commands A)

cd ../input


cat ../../_A_01_GC_content-count/input/StPGSC4.04n_seq_3_PGSC-c-rep_ITAG-cds_gff-2019-04-23.fasta ../../../_S_03_stCuSTr/_A_03.2_components/output/fasta_1A_rep-per-cv/stCuSTr-*_cds_representatives.fasta > 5cv.cds.fasta

gunzip StPGSC4.04n_seq_4_PGSC-p-rep_ITAG-pep_gff-2019-04-23.fasta.gz
cat StPGSC4.04n_seq_4_PGSC-p-rep_ITAG-pep_gff-2019-04-23.fasta ../../../_S_03_stCuSTr/_A_03.2_components/output/fasta_1A_rep-per-cv/stCuSTr-*_aa_representatives.fasta > 5cv.aa.fasta


cd ../intermediate

#################
### cdhit-est ###
#################
/home/administrator/conda2/bin/cd-hit-est -i 5cv.cds.fasta \
-o stCuSTr_cds_repAlt_cdhitEST-conda_aS.75_c.90 \
-G 1 -n 9 -g 1 -c 0.90 -aS 0.75 -p 1 -bak 1 -d 200 -b 51 -uS 0.25 \
-M 0 -T 28;
### 97553  clusters

# now run 
## chunks: libraries, f-ctions and cdhit-est 1 - cdhit-est 10

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