Building them requires zlib development files to be installed on the build machine you may need to ensure a package such as zlib1g-dev (on Debian or Ubuntu Linux) or zlib-devel (on RPM/yum-based distributions) is installed. Samtools and HTSlib depend on the zlib library. 3.The gzgetc() function is part of zlib, which is a dependency of samtools. The %GC and %AT content for AT1G01010 gene is 38.60% and 61.37% respectively. #1_usercol 2_usercol 3_usercol 4_usercol 5_usercol 6_usercol 7_usercol 8_usercol 9_usercol 10_pct_at 11_pct_gcĬhr1 phytozome9_0 gene 3631 5899. After each column in -a file, the output contains columnsįor number of overlapped features from -b file, the number of overlapped bases from -b file, length of featureįrom -a file, and their covered fractions (0 to 1 scale).Ĭut - f1 - 11 gc_content. Many bases are covered (breadth of coverage), and their covered fractions (0 to 1 scale).īy default, all features from -a file are reported in output. On coverage analysis such as how many features from -b file overlapped with -a file (depth of coverage), how Basically, it is similar to intersect but give detailed reports bed Chr1 3996 4276 2 1, 3 1 0 1 # overlapped in first and third bed filesĬhr1 4486 4605 1 1 1 0 0 Chr1 4706 5095 2 1, 3 1 0 1 # overlapped in first and third bed filesĬhr1 5174 5300 1 1 1 0 0 Chr1 5300 5326 3 1, 2, 3 1 1 1 # overlapped in all three bed filesĬhr1 5439 5630 2 1, 2 1 1 0 # overlapped in first two bed filesĬhr1 7942 7987 1 2 0 1 0 Chr1 8236 8325 1 2 0 1 0 Chr1 8417 8464 1 2 0 1 0 Chr2 5439 5630 1 3 0 0 1 3.3 Calculate the depth and breadth of coverageīedtools coverage utility helps you to calculate both depth and breadth of coverageīetween features between two BED, GFF, or VCF files. bed - header # outputĬhrom start end num list ath_cds_1. Learn more about Linux commands for Bioinformatics 2.1 Install on Linux (Ubuntu)īedtools multiinter - i ath_cds_1. The easiest way to install bedtools using package managers such as How to install bedtoolsīedtools is available only for Linux and Mac. ![]() bedtools adjusts the coordinates accordingly if the input is in GFF or VCF file formats. ![]()
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