I'm experiencing some issues with Kraken, basically I don't get any output (the sample works fine though).
I previously aligned two genomes with Satsuma (genome_v1 and genome_v2). I would like to feed Kraken with some coordinates on genome_v1 and get the corresponding on genome_v2
alignment: satsuma_summary.chained.out
first genome: genome_v2
second genome: genome_v1
Hello!
I'm experiencing some issues with Kraken, basically I don't get any output (the sample works fine though). I previously aligned two genomes with Satsuma (genome_v1 and genome_v2). I would like to feed Kraken with some coordinates on genome_v1 and get the corresponding on genome_v2
alignment: satsuma_summary.chained.out first genome: genome_v2 second genome: genome_v1
config file:
gtf file (coordinates that surely aligned to lycPyr7.1, see above alignment):
I run Kraken like this:
RunKraken -c genome.config -s genome.gtf -T genome_v2 -S genome_v1
I also tried to swap the source (-S) and target (-T) genomes but I always get an empty file
I wonder if it is just an error in the gtf file format or in the config file. I played a bit around with no success.
Do you have any suggestion?
Thank you very much for the help, Valentina