I have downloaded genome and gtf files from Ensembl. I have aligned my reads using hisat2. I am planning to get raw read counts using htseq count to use in deseq2. Many pipelines have used Ref GTF files for htseq count. I have a doubt as whether I should create a merged gtf file using stringtie or use ensembl gtf? Your suggestions will be helpful.
•
written
by
kousi31 •
2 answers
If you are working in a well annotated species (which seems likely if you are getting the GTF from Ensembl), then using the Ensembl annotation is almost certainly sufficient. This is particularly true if you are going to use gene level counts via htseq count - at best StringTie will detect some new isoforms of existing genes (which may or may not be correct), but likely that will be new combinations of existing exons, and since htseq doesn't distinguish between isoforms anyway, the gene level count will be the same.
I've written a bit about such considerations here - hope this is helpfull.
Log in to answer this question.
-
GTF file generated by stringtie merge has two source ensemble and stringtie
written by musk •
-
STAR: Is it ok to align with an index created from genecode but count features from gtf from ensemb…
written by simplitia •
-
How to quantify gene expression when stringtie considers two adjacent genes as single gene?
written by kousi31 •
-
Filtering in RNA-Seq to get Differentially Expressed lncRNA
written by conor93
-
Is it correct if we use htseq counts as raw read counts in DESEq2?
written by nazaninhoseinkhan
-
HTSEq-Count returns 0 counts for all genes in the counts file!
written by manish.nu •
-
Obtaining a GTF with a required set of gene IDs
written by spacer •
-
Incorporate new genes info to the reference gff file for running stringtie or equivalent program
written by bioinfo17 •
-
differentially expression analysis using raw read counts
written by ashkan
-
htseq-count produces no features amid alignment
written by bojingjia •
