failed to open BAM file
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?
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These are v.v.v.v trivial things you should not be asking here. Its either
my1_highquality.sorted.bamormy_highquality.sorted.bamThese is no file calledmy_highquality_sorted.bam.Isn't it
my_highquality.sorted.baminstead ofmy_highquality_sorted.bam?(With a dot)
my_highquality.sorted.bamThank you
Hello Fereshteh!
We believe that this post does not fit the main topic of this site.
You should really make an effort first, or do you want to post every second keystroke and typo? Oh, and this is not a bioinformatics question.
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Cheers!
You always are right Michael