Hello,
I need to use bamtofastq utility described in kallisto | bustools workflow (https://www.kallistobus.tools/install_bamtofastq.html) in order to convert bam files to fastq files for single-cell RNA-seq analysis. I also need to run the bamtofastq utility from my terminal in linux.
So, I have downloaded bamtofastq 1.1.2 (from https://support.10xgenomics.com/docs/bamtofastq), and placed the downloaded bamtofastq.man file in my /home/me/ directory.
From https://support.10xgenomics.com/docs/bamtofastq, they suggested to chmod 700 to make it executable. So, I did as below:
chmod 700 /home/me/bamtofastq.man
export PATH=/home/me/bamtofastq/:$PATH
bamtofastq -h
But, I faced with -bash: bamtofastq: command not found ERROR. As I am new in linux and bash, would you please help me what I did wrong and how I can install bamtofastq utility to use in my terminal?
Thank you so much. Best wishes
This is a binary. Place it into any folder of your choice, then use chmod +x bamtofastq to make it executable and run via ./bamtofastq. Add it to path as export PATH=$PATH:/path/to/folder/where/bamtofastq/is/in. PATH is always the enclosing folder, never the executable itself.
As a side note I do not think that the name of the senior author is an appropriate tag, therefore I removed it ;-)
Thank you so much for your great guide. I placed bamtofastq.man file to /scratch/me/scRNA1/ directory, and as you mentioned, I did as below, but again I faced with Error :
chmod +x /scratch/me/scRNA1/bamtofastq.man
export PATH=$PATH:/scratch/me/scRNA1/
./bamtofastq.man
bamtofastq v1.1.2 Invalid arguments.
Usage: bamtofastq [options] <bam> <output-path> bamtofastq (-h | --help)
and again bamtofastq command not found. I would appreciate your help.
bamtofastq.man? The link you specified points to a binary file named bamtofastq, so where are you getting this bamtofastq.man?bamtofastq.man -h. If that works, run mv /scratch/me/scRNA1/bamtofastq.man /scratch/me/scRNA1/bamtofastq and you should be able to use bamtofastq instead of bamtofastq.man as the command.Many thanks. I downloaded bamtofastq.man from this https://support.10xgenomics.com/docs/bamtofastq site, and I just clicked on Download bamtofastq 1.1.2 icon in the Download & Installation part.
May I kindly ask what do you mean by I am not passing any arguments? what are these arguments and how should I pass them?
Thanks a lot.
When you try to run a program you need to provide some input (and output file(s)) for the program to do its work on. These are called arguments.
If you run bamtofastq -h you can see what input the program minimally is expecting from you to be able to run in the usage statement it prints:
$ ./bamtofastq
bamtofastq v1.1.2
Invalid arguments.
Usage:
bamtofastq [options] <bam> <output-path>
bamtofastq (-h | --help)
So now if you add a -h you get:
$ ./bamtofastq -h
bamtofastq v1.1.2
10x Genomics BAM to FASTQ converter.
Usage:
bamtofastq [options] <bam> <output-path>
bamtofastq (-h | --help)
(Parts truncated)
Options:
--locus=<locus> Optional. Only include read pairs mapping to locus. Use chrom:start-end format.
--reads-per-fastq=N Number of reads per FASTQ chunk [default: 50000000]
--gemcode Convert a BAM produced from GemCode data (Longranger 1.0 - 1.3)
--lr20 Convert a BAM produced by Longranger 2.0
--cr11 Convert a BAM produced by Cell Ranger 1.0-1.1
--bx-list=L Only include BX values listed in text file L. Requires BX-sorted and index BAM file (see Long Ranger support for details).
-h --help Show this screen.
So your bamtofastq command will need to have (option(s) from the list above, if needed), name of your bam file and a path/filename(s) to store convered fastq reads at.
Log in to answer this question.
