![\"\u622a\u5c4f2023-06-15](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/2023-06-15-15-17-43.png?resize=640%2C102\")
<\/p>\n\u751f\u4fe1\u4eba\u4e00\u5b9a\u7528\u8fc7\u4e09\u5251\u5ba2awk\u3001grep\u3001sed\uff0c\u751f\u4fe1\u725b\u4eba\u2014\u2014\u674e\u6052\uff0c\u6839\u636eawk\u7684\u6e90\u4ee3\u7801\uff0c\u8fdb\u884c\u4fee\u4fee\u8865\u8865\u4e13\u95e8\u7528\u4e8e\u751f\u4fe1\u7684\u5c0f\u5de5\u5177\u3002<\/p>\n
\u4f5c\u8005\uff1a\u505a\u751f\u4fe1\u7684\u5e94\u8be5\u6ca1\u6709\u4eba\u4e0d\u77e5\u9053\u674e\u6052\u5927\u795e\u4e86\uff0c\u9f0e\u9f0e\u5927\u540d\u7684BWA\u57282009\u5e74\u52302019\u5e74\u77ed\u77ed10\u5e74\u7684\u5f15\u7528\u6b21\u6570\u5df2\u7ecf\u63a5\u8fd120K\u4e86\uff0c\u8fd9\u6837\u7684\u5f15\u7528\u6b21\u6570\u5bf9\u4e8e\u751f\u7269\u8f6f\u4ef6\u6765\u8bf4\u7edd\u5bf9\u662f\u6570\u4e00\u6570\u4e8c\u7684\u4e86\u3002\u674e\u6052\u7684\u6587\u7ae0\u968f\u968f\u4fbf\u4fbf\u5c31\u662f\u51e0\u5343\u7684\u5f15\u7528\u3002\u6700\u9ad8\u7684\u4e24\u7bc7\u5f15\u7528\u4e0a\u4e07\u6b21\u7684\uff0c\u5206\u522b\u662fBWA\u548cSAMtools\u5bf9\u5e94\u7684\u6587\u7ae0\u3002\u771f\u7684\u5f88\u611f\u8c22\u5927\u4f6c\u7ed9\u4e88\u6211\u4eec\u7684\u4fbf\u5229\uff0c\u5feb\u6765\u5b66\u4e00\u4e0b\u8fd9\u4e2a\u8f6f\u4ef6\u7684\u7b80\u4fbf\u529f\u80fd\u53ed\uff5e<\/p>\n
\u9996\u5148\uff0c\u6bd4bioawk\u662f\u5728Linux\u73af\u5883\u4e2d\u4f7f\u7528\u7684\uff0c\u63a8\u8350\u4f7f\u7528conda\u5b89\u88c5\u3002\u4e00\u884c\u547d\u4ee4\u5c31\u641e\u5b9a\uff0cconda\u7684\u4f7f\u7528\u8981\u7528-p\u6307\u5b9a\u5b89\u88c5\u76ee\u5f55\u3002
\n\u5b89\u88c5\u547d\u4ee4\uff1a\u00a0connda install -p ~\/conda path\/ bioawk -y<\/p>\n
-c\u6307\u5b9a\u6587\u4ef6\u683c\u5f0f\uff1a\u5e38\u7528\u7684\u6709bed\u3001sam\u3001vcf\u3001gff\u3001fastax<\/p>\n
-c –help\uff0c\u67e5\u770b\u53ef\u4ee5\u7528\u7684\u683c\u5f0f\uff0c\u5728\u4f7f\u7528\u8fc7\u7a0b\u4e2d\u5982\u679c\u5bf9\u683c\u5f0f\u4e0d\u6e05\u695a\uff0c\u53ef\u4ee5\u53cd\u590d\u67e5\u770b\u786e\u5b9a\u3002<\/p>\n
$ bioawk -c –help<\/p>\n
bed:<\/p>\n
1:chrom 2:start 3:end 4:name 5:score 6:strand 7:thickstart 8:thickend 9:rgb 10:blockcount 11:blocksizes 12:blockstarts<\/p>\n
sam:<\/p>\n
1:qname 2:flag 3:rname 4:pos 5:mapq 6:cigar 7:rnext 8:pnext 9:tlen 10:seq 11:qual<\/p>\n
vcf:<\/p>\n
1:chrom 2:pos 3:id 4:ref 5:alt 6:qual 7:filter 8:info<\/p>\n
gff:<\/p>\n
1:seqname 2:source 3:feature 4:start 5:end 6:score 7:filter 8:strand 9:group 10:attribute<\/p>\n
fastx:<\/p>\n
1:name 2:seq 3:qual 4:comment<\/p>\n
<\/p>\n
\u5b89\u88c5\u597d\u540e\uff0c\u5c31\u53ef\u4ee5\u7740\u624b\u4f7f\u7528\u4e86\uff0c\u5c0f\u679c\u603b\u7ed3\u4e86\u4e00\u4e9b\u5728\u751f\u4fe1\u5206\u6790\u8fc7\u7a0b\u4e2d\u53ef\u4ee5\u5e94\u7528\u7684<\/p>\n
\u4e0b\u9762\u5c31\u901a\u8fc7\u4e00\u4e2a\u4f8b\u5b50\u6765\u5c55\u793a<\/p>\n
#\u9996\u5148\u51c6\u5907\u4e00\u4e2afastq\u683c\u5f0f\u7684\u6587\u4ef6<\/p>\n
$ cat sample.fastq<\/p>\n
@A01403:54:HL3WFDRXY:1:2101:8983:1204 1:N:0:AGACCGTA<\/p>\n
AACGGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGTCAACTAGCCGTTGGGGTCCTTGAGACTTTAGTGGCGCAGCTAACGCATTAAGTTGACCGCCTGGGGAGTACGGCCGCAAGGTTAAAACTCAAATGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGATGCAAAGCGAAGAACCTTACCAGGGCTTGACATGCCGCGAATCCTCTTGAAAGAGAGGGG<\/p>\n
+<\/p>\n
FFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF,FFFFFFFFFFFFFFFFF,FFFFFFFFFFFF<\/p>\n
@A01403:54:HL3WFDRXY:1:2101:16866:1485 1:N:0:AGACCGTA<\/p>\n
AACGGGATTAGATACCCTGGTAGTCCACGCCGTAAACGATGAATGCCAGCCGTTGGTGGGTTTACTCACCAGTGGCGCAGCTAACGCTTTAAGCATTCCGCCTGGGGAGTACGGTCGCAAGATTAAAACTCAAAGGAATTGACGGGGGCCCGCACAAGCGGTGGAGCATGTGGTTTAATTCGACGCAACGCGCAGAACCTTACCAGCCCTTGACATGTCCAGGACCGGTCGCAGAGATGTGACC<\/p>\n
+<\/p>\n
FFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFF,FFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFF:FFFF:FFFFFFFFF:FFFF:<\/p>\n
![\"\u622a\u5c4f2023-06-15](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/2023-06-15-15-19-15.png?resize=640%2C119\")
<\/p>\n
#-c fastx \u6307\u793a\u51fa\u76f8\u5e94\u7684\u683c\u5f0f\uff0c\u6253\u5370\u51faname\u5217\u548cseq\u7684\u957f\u5ea6\u3002<\/p>\n
$ bioawk -c fastx ‘{print $name”\\t” length($seq)}’ sample.fastq<\/p>\n
![\"\u622a\u5c4f2023-06-15](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/2023-06-15-15-19-57.png?resize=640%2C44\")
<\/p>\n
\u662f\u4e0d\u662f\u5f88\u65b9\u4fbf\uff0c\u63a5\u4e0b\u6765\u518d\u6765\u63a2\u7d22\u4ee5\u4e0b\u5176\u5b83\u7684\u529f\u80fd\u53ed\uff5e<\/p>\n
\u53d6\u7279\u5b9a\u957f\u5ea6bp\u7684\u5e8f\u5217<\/p>\n
\u53d6\u51fa\u5927\u4e8e200bp\u5e8f\u5217\u7684id \uff0c\u5e8f\u5217\u7b49\u7b49<\/p>\n
$ bioawk -c fastx ‘length($seq)>200{print $name}’ sample.fastq<\/p>\n
![\"\u622a\u5c4f2023-06-15](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/2023-06-15-15-22-20.png?resize=640%2C76\")
<\/h4>\n$ bioawk -c fastx ‘{print “>ASV” $name; $seq}’ sample.fastq<\/p>\n
![\"\u622a\u5c4f2023-06-15](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/2023-06-15-15-23-26.png?resize=640%2C72\")
<\/p>\n
$ bioawk -c fastx ‘{print $name,gc($seq)}’ sample.fastq<\/p>\n
![\"\u622a\u5c4f2023-06-15](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/2023-06-15-15-23-55.png?resize=640%2C75\")
<\/p>\n
\u6309bioawk\u7684\u539f\u7406\uff0c\u8fd9\u4e2a\u8f6c\u5316\u5c06\u53d8\u5f97\u975e\u5e38\u7684\u7b80\u5355\uff0c\u5c0f\u4f19\u4f34\u4eec\u53ef\u4ee5\u81ea\u5df1\u601d\u8003\u4e00\u4e0b\uff0c\u6216\u8005\u53ef\u4ee5\u7528\u4f60\u719f\u6089\u7684\u7f16\u7a0b\u8bed\u8a00\u5b9e\u73b0\u4e5f\u662f\u53ef\u4ee5\u7684\u54e6\uff5e<\/p>\n
$ bioawk -c fastx ‘{print “>”$name;print $seq }’ sample.fastq<\/p>\n
![\"\u622a\u5c4f2023-06-15](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/2023-06-15-15-39-12.png?resize=640%2C68\")
<\/p>\n
\u662f\u4e0d\u662f\u5f88\u7b80\u5355\u7684\u4e00\u53e5\uff0c\u771f\u7684\u662f\u592a\u65b9\u4fbf\u4e86\uff0c\u518d\u63a5\u89e6\u8fd9\u4e2a\u8f6f\u4ef6\u4e4b\u524d\u5c0f\u679c\u4e5f\u5c1d\u8bd5\u7528\u5176\u5b83\u7684\u65b9\u5f0f\u8fdb\u884cfastq\u4e0efasta\u4e4b\u95f4\u7684\u8f6c\u5316\uff0c\u4f8b\u5982\uff1b<\/p>\n
cat sample.fastq |paste – – – – |cut -f 1,2|sed ‘s\/^@\/>\/’|tr “\\t” “\\n”|awk ‘{print $1}’>gene.fa<\/p>\n
![\"\u622a\u5c4f2023-06-15](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/2023-06-15-15-41-09.png?resize=640%2C60\")
<\/p>\n
bioawk -cfastx ‘BEGIN{while((getline k <“id.txt”)>0)i[k]=1}{if(i[$name])print “>”$name”\\n”$seq}’ sample.fastq<\/p>\n
![\"\u622a\u5c4f2023-06-15](\"https:\/\/i0.wp.com\/www.biocloudservice.com\/wordpress\/wp-content\/uploads\/2024\/01\/2023-06-15-17-05-21.png?resize=640%2C41\")
<\/p>\n
\u8fd9\u91cc\u7684id.txt\u5b58\u653e\u7684\u662f\u4e0d\u5e26\u201c>\u201d\u7684id<\/p>\n
bioawk -c fastx ‘length($seq) > 10 {print “@”$name”\\n”$seq”\\n+\\n”$qual}’ input.fastq<\/p>\n
\u5c06\u672a\u6bd4\u5bf9\u4e0a\u7684\u5e8f\u5217\u63d0\u53d6\u51fa\u6765\uff1abioawk -c sam ‘and($flag,4)’ input.sam<\/p>\n
\u5c06\u6bd4\u5bf9\u4e0a\u7684\uff08mapped\uff09\u5e8f\u5217\u63d0\u53d6\u51fa\u6765\uff1abioawk -c sam -H ‘!and($flag,4)’ input.sam<\/p>\n
\u6839\u636esam\u6587\u4ef6\u521b\u5efafasta\uff1abioawk -c sam ‘{ s=$seq; if\uff08and($flag,16)\uff09{s=revcomp($seq)} print “>”$qname\u201c\\n\u201ds’ input.sam > out.fasta<\/p>\n
#\u8fd9\u91ccsam\u53ef\u80fd\u4f1a\u5b58\u5728\u53cd\u5411\u5e8f\u5217\uff0c\u5982\u679cflag=16\u4e3a\u53cd\u5411\u5e8f\u5217\uff0c\u9700\u8981\u5148\u7528revcomp\u8fdb\u884c\u53cd\u8f6c\u540e\u518d\u8d4b\u503c\u7ed9s\uff0c\u6700\u540e\u6253\u5370\u51fa\u540d\u5b57\u548c\u76f8\u5e94\u7684\u5e8f\u5217\u5373\u53ef\u3002<\/p>\n
\u6839\u636e\u4e0a\u8ff0\u7684\u5b9e\u8df5\u64cd\u4f5c\uff0c\u53ef\u4ee5\u76f4\u89c2\u7684\u611f\u53d7\u5230\u5c0f\u5c0f\u7684\u8f6f\u4ef6\uff0c\u4f46\u6db5\u76d6\u7684\u529f\u80fd\u662f\u975e\u5e38\u7684\u5f3a\u5927\u7684\u3002\u5728\u6570\u636e\u5904\u7406\u4e2d\u4e0d\u514d\u4f1a\u9047\u5230\u5404\u79cd\u5404\u6837\u7684\u95ee\u9898\uff0c\u6709\u65f6\u5019\u5199\u4ee3\u7801\u4f1a\u5f88\u7e41\u7410\u5e76\u4e14\u5bb9\u6613\u51fa\u73b0bug\u3002\u4e0d\u59a8\u5728\u5e73\u65f6\u591a\u591a\u79ef\u7d2f\u4e00\u4e9b\u597d\u7528\u7684\u751f\u4fe1\u8f6f\u4ef6\u534f\u52a9\u6211\u4eec\u89e3\u51b3\u95ee\u9898\u3002\u8fd9\u79cd\u5927\u4f6c\u5f00\u53d1\u7684\u4e13\u95e8\u7528\u4e8e\u751f\u7269\u4fe1\u606f\u5b66\u5206\u6790\u7684\u8f6f\u4ef6\uff0c\u4e0d\u4ec5\u80fd\u591f\u5feb\u901f\u7684\u4e86\u89e3\u751f\u7269\u4fe1\u606f\u5b66\u4e2d\u7684\u6587\u4ef6\u683c\u5f0f\uff0c\u5e76\u4e14\u4e0a\u624b\u7b80\u5355\uff0c\u975e\u5e38\u9002\u5408\u5c0f\u767d\u7684\u5b66\u4e60\u3002<\/p>\n
\u597d\u4e86\uff0c\u8fd9\u6837\u6211\u4eec\u5c0f\u8f6f\u4ef6\u7684\u5206\u4eab\u5c31\u5230\u8fd9\u91cc\u53ed\u3002\u5c0f\u4f19\u4f34\u4eec\u5982\u679c\u6709\u4ec0\u4e48\u95ee\u9898\u5c31\u548c\u5c0f\u679c\u8ba8\u8bba\u5427\u3002<\/p>\n","protected":false},"excerpt":{"rendered":"
bioawk\u7b80\u4ecb \u751f\u4fe1\u4eba\u4e00\u5b9a\u7528\u8fc7\u4e09\u5251\u5ba2awk\u3001grep\u3001sed\uff0c\u751f\u4fe1\u725b\u4eba\u2014\u2014\u674e\u6052\uff0c\u6839\u636eawk\u7684\u6e90\u4ee3\u7801\uff0c\u8fdb\u884c\u4fee\u4fee […]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"jetpack_post_was_ever_published":false,"_jetpack_newsletter_access":""},"categories":[1],"tags":[],"jetpack_featured_media_url":"","_links":{"self":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24056"}],"collection":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=24056"}],"version-history":[{"count":1,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24056\/revisions"}],"predecessor-version":[{"id":24073,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=\/wp\/v2\/posts\/24056\/revisions\/24073"}],"wp:attachment":[{"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=24056"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Fcategories&post=24056"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/www.biocloudservice.com\/wordpress\/index.php?rest_route=%2Fwp%2Fv2%2Ftags&post=24056"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}