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lines changed Original file line number Diff line number Diff line change @@ -121,4 +121,25 @@ two output will be generated
121121* Ensembl.str.sqlite_two_step.pergeno.mutated_protein.fa
122122
123123Note:
124- if variant is a string, the ` -S ` option is required.
124+ if variant is a string, the ` -S ` option is required.
125+
126+ ## CHM13 T2T from RefSeq
127+
128+ Since the data is in the same format like RefSeq, we tested the command below and it works perfectly.
129+
130+ ``` Python
131+ cd $ PATH_OF_PRECISONPRODB
132+
133+ python ./ src/ downloadHuman.py - d CHM13 - o precisionprodb
134+
135+ python ./ src/ PrecisionProDB.py \
136+ - g precisionprodb/ GCF_009914755 .1_T2T- CHM13v2.0_genomic.fna.gz \
137+ - p precisionprodb/ GCF_009914755 .1_T2T- CHM13v2.0_protein.faa.gz \
138+ - t 12 \
139+ - a RefSeq \
140+ - f precisionprodb/ GCF_009914755 .1_T2T- CHM13v2.0_genomic.gtf.gz \
141+ - m precisionprodb/ Jurkat.CHM13 .RefSeq.vcf.gz \
142+ - o precisionprodb/ Jurkat.CHM13 .RefSeq.PrecisonProDB \
143+ - S precisionprodb/ GCF_009914755 .1_T2T- CHM13v2.0.sqlite
144+ ```
145+
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