IGV viewer could not display genome sequences correctly

Question

[xiaoleiusc]

Dear All,

Although I updated my IGV viewer to the newest version (2.8) in my MacOS, it could not display genome sequences correctly, it displays each base in the sequence as little squares at the bottom " sequence" track.

I attach a screenshot here ( https://photos.app.goo.gl/Vn2wtDgkh1xhgufR7 ).

Any input is appreciated.

Thanks ahead,

Xiao

[JC]

looks like a missing font for Java

[Pierre Lindenbaum]

how was formatted you fasta sequence

can you verifiy that the chromosome is present in the *.fasta , *.fai and the *.dict files.

[xiaoleiusc]

Thanks for the input. I have *.fasta and *.fai files, but no *.dict file.

[xiaoleiusc]

Thanks for the input. I tried to use Picard to generate *.dict file, but the problem still exists.

[Juke34]

Move on to Jbrowse ;)

Answer 1

[xiaoleiusc]

Thanks all for the inputs. Igv developer solved the problem, I pasted the solution here:

OK, the problem is your fasta file is missing a line feed at the end of the file. This is a problem because the index (fai) file says there are 9179 bases, and 9180 bytes in each line. So that last byte (the line feed) has to be present, otherwise IGV will try to read past the end of the file. Open the fasta file in a text editor, go the end of the file, hit a carriage return then save it.

Answer 2

[Jim Robinson]

The problem generally indicates that sequence could not be read, or is not present for the location visited. It can indicate a problem with the fasta index, but usually it is caused by a proxy or firewall blocking the S3 buckets from which we serve the sequence.