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Old 07-30-2012, 01:47 PM   #1
lj907
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Location: Boston, MA

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Default sh: samtools: command not found (Tophat)

Dear all,

I have been using tophat for my RNA-seq data. The command line I'm using is the standard: ./tophat -p 8 -G /path_to_genes.gtf/ -o <output_folder> /path_to_genome_index/ XXX.fastq

Tophat runs happily, finds bowtie and samtools, checks for bowtie index, Fasta reference, generates SAM header... all goes well and I have 4 outputs: accepted_hits.bam deletions.bam insertions.bam and junctions.bam... However, when the sam version of accepted_hits.bam is going to be written, samtools fails and I get a message saying sh:samtools: command not found...
Having gone through with the bam files till the very end (cufflinks then cuffdiff and R), I seem to get the analysis running but I don't understand why samtools fails during the mapping.... Tophat clearly recognises it at first.. and ./samtools <options> work nicely for other applications.
Just to add I have used samtools-0.1.17.tar.bz2 (I'm on a iMac) untar ed it and cp ed it into my working path (I haven't got permission for /usr/bin), I have also cp ed libbam.a into my working directory...
Can anyone help me
Cheers
lj907
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Old 07-31-2012, 02:51 AM   #2
flxlex
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Moved to a more appropriate forum
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Old 07-31-2012, 03:05 AM   #3
maubp
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Perhaps you can add your working directory to the $PATH environment variable, if that is where your copy of samtools is?

Personally, I use $HOME/bin for things I install under my own account, and put that on the $PATH. Most Linux tools can be installed in this way, if they use a configure script try adding --prefix=$HOME to this.
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Old 07-31-2012, 10:26 AM   #4
lj907
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Cheers Peter, I'm copying executables into $HOME/bin
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