Problem Using Tabix: Tabix Can'T Find The Directory Of The Example File

Question

[Johnathan]

Hi everyone!

I am learning to use Tabix. I am interested in querying the structural genomic variations of 18 strains of mice stored on a Wellcome Trust Institute server ( ftp://ftp-mouse.sanger.ac.uk/REL-1302-SV/). The file has already been compressed using bgzip and indexed using tabix. The files are: 1) 18strains.REL-1302-SV.sdp.tab.gz 2) 18strains.REL-1302-SV.sdp.tab.gz.tbi (index)

According to the README file, I can simply type the following:

tabix  ftp://ftp-mouse.sanger.ac.uk/REL-110804-SV/18strains.REL-1302-SV.sdp.tab.gz  2:3000000-4000000

However, when I do so, I get the following error on my terminal:

trains.REL-1302-SV-GRCm38.sdp.tab.gz  2:3000000-4000000
[kftp_connect_file] 550 /REL-1302-SV/18strains.REL-1302-SV-GRCm38.sdp.tab.gz: No such file or directory
[main] fail to open the data file.

Does anyone else have similar issues?

Thank you!

[Devon Ryan]

Shouldn't the URL be: ftp://ftp-mouse.sanger.ac.uk/REL-1302-SV/18strains.REL-1302-SV.sdp.tab.gz ? The URL you specified just doesn't exist.

Answer 1

[Pierre Lindenbaum]

just look at ftp://ftp-mouse.sanger.ac.uk/REL-110804-SV: the file has been deleted.

try to play with the files under ftp://ftp-mouse.sanger.ac.uk/REL-110804-SV/all/

[Johnathan]

Thank you for your input. Yes, you are right. I didn't verify this at first because I was following the HELPME file. However, I simply downloaded the file from another path onto my computer and tabix works great now.