Entering edit mode
8.7 years ago
zizigolu
★
4.3k
Friends,
[izadi@lbox161 ~]$ bash
[izadi@lbox161 ~]$ cd /usr/data/nfs6/izadi/gij
[izadi@lbox161 gij]$ pwd
/usr/data/nfs6/izadi/gij
[izadi@lbox161 gij]$ ls
S288C_rRNA.fsa my.sam
SRR1944914.fastq my1.sam
SRR1944914.sra my1_highquality.bam
SRR1944914_trimmed.fastq my1_highquality.sam
SRR1944914_trimmed_unmapped.fastq my1_highquality.sorted.bam
SRR1944926.fastq my_highquality.bam
SRR1944926.sra my_highquality.bed
SRR1944926_trimmed.fastq my_highquality.sam
SRR1944926_trimmed_unmapped.fastq my_highquality.sorted.bam
coding.1.bt2 orf_coding.fasta
coding.2.bt2 rRNA.1.bt2
coding.3.bt2 rRNA.2.bt2
coding.4.bt2 rRNA.3.bt2
coding.rev.1.bt2 rRNA.4.bt2
coding.rev.2.bt2 rRNA.rev.1.bt2
mapped_and_unmapped.sam rRNA.rev.2.bt2
[izadi@lbox161 gij]$ export BED=/usr/people/home/izadi/fereshteh/bedtools2/bin
[izadi@lbox161 gij]$ echo $BED
/usr/people/home/izadi/fereshteh/bedtools2/bin
[izadi@lbox161 gij]$ $BED/bamToBed -i my_highquality_sorted.bam > my_highquality.bed
Failed to open BAM file my_highquality_sorted.bam
What is the reason please?