Hi,
Two questions:
1) I'm trying to figure out if the RNA-seq data generated from this study was stranded. Would be helpful for anyone trying to generate different counts datatypes with the provided bam files.
2) Also, the already generated counts data directories indicate that tophat and bowtie were used to align the data to hg19, but in the parent directories, it indicates that SNAPR was used to align to GRCh38. Which is it?
Thanks!
Created by Michael Nagle naglem1 Hi,
Thanks for the quick responses. Is it possible to get access to the older TopHat/Bowtie aligned bam files? The algorithm I'm attempting to use is having a hard time dealing with the SNAPR alignments. Thanks.
Mike Hi Michael
The count data and aligned bam files provided in syn5550404 were aligned using SNAPR.
There are differential expression results provided in (syn6090802 and syn7332090) that are based on gene counts aligned using TopHat/Bowtie. These were generated separately from the SNAPR counts, although on the same subjects.
Mariet Hi Michael,
The RNA-seq data is not stranded. Everything under that Synapse ID was aligned using SNAPR. There are older datasets that were aligned with TopHat/Bowtie. Dear Michael,
I have contacted @coryfunk and @mxa24 who should be able to answer your question.
Best,
Ben