I have ran Tophat on 50bp paired-end Illumina data and it generates quite a few warnings as below.
[Thu Mar 3 09:35:27 2011] Indexing splices
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
many more lines of this.
Is this something to be concerned about? I am using HG19 which was indexed using the latest Bowtie-build;
bowtie-build version 0.12.7
TopHat v1.2.0
Thanks for any tips.
John.
[Thu Mar 3 09:35:27 2011] Indexing splices
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
Warning: Encountered reference sequence with only gaps
many more lines of this.
Is this something to be concerned about? I am using HG19 which was indexed using the latest Bowtie-build;
bowtie-build version 0.12.7
TopHat v1.2.0
Thanks for any tips.
John.