Is there a way how to map one fas file (100 short sequences) on a dataset (fas files) of a few large seqences and then count how many short hits hit which large sequence? In other words, to test off-target effect of RNAi.
Thanks
Jan Perner
BLAST should be able to do this. You can also try to use mapping tools like bowtie2 or bwa for it and provide your reference genome as FASTA file I guess.
Dne 20.11.2014 19:16, Bjoern Gruening on Galaxy Biostar napsal(a): Dear Bjoern, thank you for your response. However, I failed to find blast in galaxy progream list and mapping programs striclty require fastQ files. Regards Jan
This is true, Blast is not installed on usegalaxy.org. But you can take a mapper. Your reference genome can be in fasta format and for your input you either can try to convert your FASTA file into FASTQ with uniquely assigned quality values or wait until we have released the new version of our wrappers with FASTA support.
