Entering edit mode
3.9 years ago
dott.difranco
•
0
Hello everybody I'm new in this word of bionformatic and I'd want found structural variant on my bam file (that is stored in external HD) with breakdance. I've read this guide, but when I launch the first script:
/usr/lib/breakdancer-max1.2/bam2cfg.pl bam_files breakdancer_options
I've the file or directory not found. I've installed Perl v5.26.1
Where is my error? Thanks
Either the
bam2cfg.pldoes not exist at the location above, or one or more of the BAM files do not exist. If there are any files that are part of thebreakdancer_optionsparameter, check that they all exist too.The file bam2cfg.pl exist in this path:
home/marcoubu/breakdancer-master/perl/bam2cfg.pl. The file .bam exist too:media/sf_hd500gb/genoma S17-530.Can you please give us the exact command you're using?
I'm using this commad (from https://gmt.genome.wustl.edu/packages/breakdancer/documentation.html):
/usr/lib/breakdancer-max1.2/bam2cfg.pl bam_files breakdancer_options
Howerver, on going, I've seen that in /usr/lib I don't find the folder breakdancer-max1.2, but this is strange because the installation was successful. Also, I have seen that the file "bam2cfg.pl" is located only in /breakdancer/perl. What should I do to run the software? Thank you so much for your answers.
That "command" is a template, it's not a real command.
bam_filesandbreakdancer_optionsare placeholders for real parameter values. The command under STEP 1 is a real command (/usr/lib/breakdancer-max/bam2cfg.pl -g -h tumor.bam normal.bam > BRC6.cfg).Your install location is different from the one specified in the manual. Your answer to where the
.bamfiles exist doesn't seem accurate (unless you have a blank space in the directory namegenoma S17-530. Your answer to wherebam2cfg.plexists seems to be inaccurate too (probably a copy-paste error - it might be/home/andhome/).You'll need something along these lines:
First of all thank you for the technical support. I haven't make past and cut.
So, I tried the following command (because my file bam is in this path /media/sf_hd500gb):
but I've this long error message:
....and a simil message I've when I launched
I don't know if it may help you to know that I find the breakdancer-max folder in:
What am I doing wrong?
Thanks a lot.
You should talk to someone near you that understands Linux. You're literally passing "actual_breakdancer_options", and there is no way I can make you understand what I'm trying to convey. It's like I'm telling you "Tell me your actual name" and you're replying with "your actual name". It's starting to get silly now.
I have no idea why you're passing in the
S17-530string, and again, you need someone near you that knows Linux. They'll be able to help you better than anyone over the Internet can.Unfortunately I don't have any friends who know linux. From your experience do you think it is impossible for me to undertake the SV reading of my genome?
It's your own genome? And you are going to dive into the data when you can't run a very basic command? With all respect, but that's highly irresponsible. You need someone with more experience. You can do whatever the hell you want with your own genome, but what do you aim to find?
By "my genome" I meant the genome I need to test. My professor gave me this task and I should finish it. If you can help me, thank you. Nice day
It will be quite challenging to run command line tools without a basic understanding of how the command line works, or how to read and understand command line documentation. I looked for an online version of breakdancer that doesn't need command line knowledge, but it looks like Galaxy might not have it. I'd encourage you to do some more digging to check for any SV detection tool that has a graphical interface, find someone that knows the command line or learn command line basics.
If your professor gave you this task, they believe you have the skill to do this and they will be open to helping you out now that you're having genuine difficulties.
Thanks a lot RamRS. Nice day
May be you can change the "bam_files " to your real bam path. like /home/xx/work/xx.bam.