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term3 🕒

Bedtools

TASK1. Обязательная часть 
команда
 
описание
 
/P/y14/term3/block4/SNP/bedtools2/bin/bedtools bamtobed -i 
sortalignrna.bam > reads.bed
 
Convert BAM alignments to BED format.
Выходной файл:reads.bed
 
/P/y14/term3/block4/SNP/bedtools2/bin/bedtools intersect -a 
reads.bed -b /P/y14/term3/block4/SNP/rnaseq_reads/gencode.genes.bed -u > both2.bed

Report whether each alignment overlaps one or more genes. 
If not, the alignment is not reported.
Выходной файл:both2.bed
 
/P/y14/term3/block4/SNP/bedtools2/bin/bedtools intersect -a 
reads.bed -b /P/y14/term3/block4/SNP/rnaseq_reads/gencode.genes.bed -c > both.bed
 
Report the number of genes that each alignment overlaps.
Выходной файл:both.bed
 
/P/y14/term3/block4/SNP/bedtools2/bin/bedtools intersect -b 
reads.bed -a /P/y14/term3/block4/SNP/rnaseq_reads/gencode.genes.bed -u > both3.bed

Report whether each alignment overlaps one or more genes. 
If not, the alignment is not reported.
Выходной файл:both3.bed
 

ген		размер 		Bases covered:		координаты		функция					количество экзонов	направление

ALDH1A2		324,007/318,006 (98.15%)		chr15:57,955,197	The product of this gene is an enzyme           13               обратное
							-58,279,203		that catalyzes the synthesis of retinoic 
										acid (RA) from retinaldehyde.

CTD-2330J20.2   5,819/5,819 (100.00%)             chr15:58,357,423-58,363,241                                    -                   -
TASK2. Дополнительная часть 
номер задания
 
команда
 
описание
 
1
 
/P/y14/term3/block4/SNP/bedtools2/bin/bedtools 
bamtofastq -i sortalignrna.bam -fq reads.fastq
 
bedtools bamtofastq is a conversion utility for extracting FASTQ records 
from sequence alignments in BAM format
Выходной файл:reads.fastq
 
5
 
/P/y14/term3/block4/SNP/bedtools2/bin/bedtools random -l 200 -n 1000 -g 
chr15.fasta.fai > random.bed
 
bedtools random will generate a random set of intervals in BED6 format. 
One can specify both the number (-n) and the size 
(-l) of the intervals that should be generated
Выходной файл:random.bed
 
3
 
/P/y14/term3/block4/SNP/bedtools2/bin/bedtools makewindows -g chr15.fasta.fai
-w 1000000 > windows.bed
wc -l windows.bed
 
Count how many exons occur in each 1000kb interval (“window”) in the chr15 of human genome.Ответ=103.
длина хромосомы в нуклеотидах равна  102531392(инфа есть в файле chr15.fasta.fai)
Выходной файл:windows.bed

© Цыганов Кирилл, 2017