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1.gtf与Bed的互相转换, 两者都是基因注释文件,gtf的一行表示一个exon,多行表示一个基因。而bed的一行表示一个基因。
$ perl gtf2Bed.pl $gtfFile >$bedFile
$ sh bedToGtf.sh $bedFile >$gtfFile
2.利用bed从基因组上取fasta
$twoBitToFa -bed=$bedFile $genome.2bit $fastaFile
补充:fasta转成2bit
$ faToTwoBit in.fa out.2bit
3.bam转成bedgraph
bedgrahp可以对bam文件进行可视化的查看,写论文时经常要截图
$ genomeCoverageBed -bg -ibam $bamFile -g $genome.sizes > $bedgraphFile
4.sam与bam的互转
bam-->sam:
$ samtools view -h -o $out.sam $in.bam
sam-->bam:
$ samtools view -bS in.sam >out.bam
5.Usage: fq_all2std.pl command in.txt Command: scarf2std Convert SCARF format to the standard/Sanger FASTQ fqint2std Convert FASTQ-int format to the standard/Sanger FASTQ sol2std Convert Solexa/Illumina FASTQ to the standard FASTQ fa2std Convert FASTA to the standard FASTQ fq2fa Convert various FASTQ-like format to FASTA instruction Explanation to different format example Show examples of various formats |
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