small RNA seq - sRNAbench
Hi,
I have two questions concerning the analysis of a small RNA seq data set.
1. The tool I would like to use to quantify miRNAs and possibly piRNAs is sRNAbench. This works well in "library mode" but when I include the reference genome (="genome mode") nothing works. No usable error outputted by the program. Has anyone used this tool in genome mode successfully and could give me some advice? The libraries I am trying to quantify are in fasta format, which should be fine.
(I already tried to rebuild the index in case that would have been an issue.)
2. Can anyone recommend similar tools to quantify miRNA/piRNA?
Thanks a lot for the help!
I have two questions concerning the analysis of a small RNA seq data set.
1. The tool I would like to use to quantify miRNAs and possibly piRNAs is sRNAbench. This works well in "library mode" but when I include the reference genome (="genome mode") nothing works. No usable error outputted by the program. Has anyone used this tool in genome mode successfully and could give me some advice? The libraries I am trying to quantify are in fasta format, which should be fine.
(I already tried to rebuild the index in case that would have been an issue.)
2. Can anyone recommend similar tools to quantify miRNA/piRNA?
Thanks a lot for the help!