분류 전체보기198 how to make reverse complement of sequence in shell file content format(tab seperate) seq_1 atgagagataac seq_2 tagcgattcaca output file format(fasta type) >seq_1 atgagagataac >seq_1_recom gttatctctcat >seq_2 tagcgattcaca >seq_2_recom tgtgaatcgcta $ cat "sequence file" | while read id seq; do echo -e ">$id\n$seq"; recom_seq=$(echo $seq | rev | tr "atgc" "tacg"); recom_id="$id"_revom; echo -e ">$recom_id\n$recom_seq"; done > outout.fasta ex) $ awk .. 2012. 3. 5. Promoter 지역에서 특정 motif 찾기 Extract Description $ grep -f TATATA.uniq.OsID /home/kimth/data/ggbio/databases/IRGSP/RAP2/gff_RAP2/RAP2.desc.txt $ while read OsID; do grep $OsID /home/kimth/data/ggbio/databases/IRGSP/RAP2/gff_RAP2/RAP2.desc.txt; done TATATA.desc.txt Extract Unique Sequence ID with Sequence $ grep Forward ATATAT.txt | cut -f1,7 | sort | uniq > TATATA.2k.txt Extract matching position $ cut .. 2012. 2. 20. Extract OsID and Description to RAP2(IRGSP4) $ sed -e "s/^locus_id \"\(.*\)\";Description \"\(.*\)\";category.*/\1\t\2/g" -e "s/^seq_id \"\(.*\)\";locus_id.*;Description \"\(.*\)\";Source.*/\1\t\2/g" RAP2.desc.txt > RAP2.gene.desc.txt 2012. 2. 17. How to update lastest R http://cran.stat.sfu.ca/bin/linux/ubuntu/ 2012. 2. 16. Velvet Fixed List Change src/globals.h #define int8_t Category -> #define int16_t Category 2012. 2. 16. Installing SGA(String Graph Assembler) on Ubuntu 10.04 Server(64bit) SGA dependencies: -google sparse hash library (http://code.google.com/p/google-sparsehash/) $ wget http://sparsehash.googlecode.com/files/sparsehash_2.0-1_amd64.deb $ sudo dpkg -i sparsehash_2.0-1_amd64.deb -the bamtools library (https://github.com/pezmaster31/bamtools) $ git clone git://github.com/pezmaster31/bamtools.git $ sudo apt-get install cmake (Skip if cmake exists) $ cmake --version (ve.. 2012. 2. 15. 이전 1 ··· 15 16 17 18 19 20 21 ··· 33 다음