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Forum: Bioinformatics 02-28-2018, 11:32 AM
Replies: 0
Views: 1,443
Posted By kuristy
Stringtie inconsistency

I am doing a large RNAseq experiment, and I am doing hisat2-stringtie-ballgown as we get new samples. After alignment and assembly, I do stringtie --merge with new samples and older samples together....
Forum: Bioinformatics 10-04-2017, 02:23 PM
Replies: 1
Views: 1,746
Posted By kuristy
I have answered my own question, but I am posting...

I have answered my own question, but I am posting just in case someone else has a similar issue.

I ran the same tophat data with stringtie and got a similarly bad correlation between technical...
Forum: Bioinformatics 10-03-2017, 09:28 AM
Replies: 1
Views: 1,746
Posted By kuristy
Hisat2 vs Tophat2 variation between tech reps

I have a question regarding the variability of FPKM I am seeing between technical replicates in the Hisat2, stringtie pipeline. When I plot technical replicates by log2 FPKM, I am getting Spearman...
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