MAIN

TERMS

PROJECTS

ABOUT

Obligatory task

Command table

Command name input output
bedtools bamtobed -i chr10.1_sorted.bam > chr10.1_sorted.bed bam file with coordinates bed file with coordinates
bedtools intersect -u -a gencode.genes.bed -b chr10.1_sorted.bed > int.bed gencode.genes.bed (genes mapping file), chr10.1_sorted.bed (sorted bed file with coordinates) intersection of genes mapping file and sorted bed file with coordinates
bedtools coverage -counts -b gencode.genes.bed -a int.bed > cov.bed intersection of genes mapping file and sorted bed file with coordinates bed file with coverage

There were 2 gene, presented in the output. One of them was a miscellaneous RNA coding gene (accession RN7SL373P, according to ensembl). The other one was a DDX21 gene. It's a gene with Nucleolar RNA helicase function. Coordinates, according to hg19: chr10:70,715,879-70,744,825 Size: 28,947 Total Exon Count: 15, Total Intron Count: 15 Strand: +. Another splice variant - coordinates: chr10:70,716,196-70,744,825 Size: 28,630 Total Exon Count: 15, Total Intron Count: 15 Strand: + Coding Region

Extra tasks

Command name input output
bedtools bamtofastq -i chr10.1_sorted.bam -fq chr10.1_sorted.fastq .bam file with alignments fastq file with reads
bedtools getfasta -fi chr10.fasta -bed gene.bed > gene.fasta .fasta file with chromosome sequence, .bed file with gene coordinates gene sequence
bedtools makewindows -g chr10_mw.genome -w 1000000 .genome file with chromosome length (135534747), chunk size number of intervals (136), coordinates of intervals
bedtools cluster -i chr10.1_sorted.bed .bed file with gene coordinates number of clusters (22)
bedtools slop -i gene.bed -g chr10_mw.genome -l 0 -r 1000 .bed file with gene coordinates, .genome file with chromosome length, length of the addition slopped gene coordinates
bedtools slop -i gene.bed -g chr10_mw.bed -b 1000 .bed file with gene coordinates, .genome file with chromosome length, length of the addition slopped gene coordinates
bedtools slop -i gene.bed -g chr10_mw.bed -l 500 -r -500 .bed file with gene coordinates, .genome file with chromosome length, length of the addition shifted gene coordinates
bedtools complement -i chr10.1_sorted.bed -g chr10_mw.genome .bed file with gene coordinates, .genome file with chromosome length coordinates of the parts, that are not overlapped by .bed file
bedtools genomecov -ibam chr10.1_sorted.bam -bg .bam file with alignments interval coordinates with coverage depth

© Gumerov Ruslan, 2017