Bioinformatics18 how to blast to nr database 다운받은 시퀀스를 seq.fa 파일에 모두 모아 blastall의 blastx 하였음. $ blastall -i seq.fa -d /home/galaxy/blastdb/nr/nr -p blastx -a 16 -e 1e-10 -m 8 -o seq.fa.blastx 2> error.log & blast된 결과중에 1st만 뽑음 $ /share/scripts/1st_highest.sh seq.fa.blastx > seq.fa.blastx.1st 1st 결과에 description 붙임. $ /share/scripts/add_desc.sh -i seq.fa.blastx.1st -d ~/blastdb/nr/nr > seq.fa.blastx.1st.desc description붙은 결과에서 ADGAL, pGAD를 .. 2012. 4. 27. usage bwa using paired-end reads make reference index/home/galaxy/galaxy-dist/bin/bwa index -p 454.bwa.index -a bwtsw assembly1/454AllContigs.fna paired-end alignment/home/galaxy/galaxy-dist/bin/bwa aln 454.bwa.index -I denovo/Gal_trim1.fastq > Gal_trim1.bwa.aln.sai/home/galaxy/galaxy-dist/bin/bwa aln 454.bwa.index -I denovo/Gal_trim2.fastq > Gal_trim2.bwa.aln.sai/home/galaxy/galaxy-dist/bin/bwa sampe 454.bwa.index Gal_trim1.bw.. 2012. 4. 5. 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. ABySS 사용시 주의점 k-mer 값을 정하는 것이 중요..k-mer 값에 의해 프로그램이 실행되거나 아님 중간에 오류가 발생할 수 있다. read의 길이를 고려해서 k-mer를 정해야함. http://www.bcgsc.ca/platform/bioinfo/software/abyss 2012. 2. 9. xys 링크파일만들기 ls -d -1 ../xys_files/*.xys | while read file;do d=$(pwd); b=$(basename $file); ln -s $d/$file $b; done 2011. 12. 14. 이전 1 2 3 다음