Off topic:failed to open BAM file
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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?

bam bed • 4.4k views
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