I have been trying to use a genome build for sheep (OviAri4 UCSC gold fasta) for mapping single end RNAseq data with bowtie2. No matter what I try, downstream use of the mapped BAM output with featurecounts fails give give any counts. I have tried all the options/advice described under the help section, but to no avail.
Any possibility that the sheep genome (and if possible the goat genome) could be added as built-ins for bowtie2?
Hi @Phil,
I informed the sysadmin in order to include both genomes; also, could you share your Galaxy history with me? I will have a look at the problem. My email is 
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Regards
Sure…
Thanks. I am curious to understand the issue I am having, so any insights are greatly wlecome.
Phil
Hi @Phil,
could you provide me with some details about the version of the goat genome that you need?
Regards
Thanks for your response.
The ARS1 Aug 2016 (San Clemente) should do the trick thanks.
Phil
Hi,
Yes, got the sheep done this morning, thanks for that!
However, for some reason the goat ARS1 2016 version is different from the GTF RefSeq version resulting in no feature counts again. Seems that the NCBI RefSeq GTF uses GCF_001704415.1 and the version that you guys have kindly installed is GCF_001704415.2, at least that’s the only difference I can see.
Anyway, thanks again for the Sheep, that solved my issues… just have to find a work around for the goat I guess.
Phil
We will include that one also.
Regards
Wow, that would be great!
Thanks!
Phil