比如说ChIP-seq得到的peaks可以根据“距离其最近的基因就是他调控的基因”的假设进行注释。 coverage: 计算某个区间的覆盖情况 genomecov: 计算全部基因组的覆盖情况 map: 在某个区间的应用其他函数, 比如说求和(sum), 均值(mean) annotate: 从其他一系列文件中统计给定区间的覆盖情况 区间工具: flank: 根据已有特...
比如说ChIP-seq得到的peaks可以根据“距离其最近的基因就是他调控的基因”的假设进行注释。 coverage: 计算某个区间的覆盖情况 genomecov: 计算全部基因组的覆盖情况 map: 在某个区间的应用其他函数, 比如说求和(sum), 均值(mean) annotate: 从其他一系列文件中统计给定区间的覆盖情况 区间工具: flank: 根据已有特...
Bedtools coverage命令可以计算BED文件B在A文件上覆盖的深度和广度。例如bedtools coverage可以计算B文件在A文件特定的1kb窗口上的覆盖情况。Coverage命令的一大优势是它不仅计算与A文件各特征的重叠数目,而且计算重叠的比例。此外coverage也计算了与A文件各个区间重叠的区域的大小。 示例: bedtools coverage[OPTIONS]-a<F...
To get an esimate of mean coverage for a contig we sum (Depth of coverage) * (Number of bases on contig) / (Length of the contig). We have a quick script that will do this calculation. 计算平均深度 wget https://raw./ngs-docs/2017-cicese-metagenomics/master/files/calculate-contig-cov...
55、force strandedness -scores str how to determine the scores of the merged sum, min, max, mean, median, mode, antimode, collapse slopbed slopbed -i in.bed -g genome 将feature向两侧扩展 -b int/float in each direction -l int/float in left (upstream) direction -r int/float in righ...
mean | pigz -p 1 > "AB_udghalf_libmerged_rmdup".depth.gz Command exit status: 1 Command output: (empty) Command error: Error: Sorted input specified, but the file Homo_sapiens.GRCh37.87.gff3 has the following record with a different sort order than the genomeFile genome.txt GL000192.1...
4 consensus base 5 consensus quality 6 SNP quality 7 root mean square (RMS) mapping quality 8 read coverage/depth 9 read bases 10 alignment mapping qualities samtools pileup an indel occupies an additional line (-i) 1 chromosome same 2 coordinate 3 just '*' 4 genotype 5 consensus quality ...
debug('Sample average depth is too low (less than '+ str(AVG_DEPTH_THRESHOLD_TO_DETERMINE_SEX) +') - cannot determine sex')returnNoneifchry_mean_coverage ==0: debug('Y depth is 0 - it\s female') sex ='F'else: factor = avg_depth / chry_mean_coverage ...
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bedtool = bedtool.filter(lambdax: (x.fields[3].split(",")[1]!="INS"or((min_ins_cov_frac*mean_read_coverage)<=(float(x.fields[6])/abs(x.start-x.end+1)*mean_read_length)<=(max_ins_cov_frac*mean_read_coverage))).moveto(coverage_filtered_bed) func...