strand-specific RNA-seq analysis
my RNA-seq data :Total RNA (1μg) from each cell type was used to generate next generation RNA-seq libraries using Illumina TruSeq stranded library preparation kit per manufacturer’s protocol by RNA ligation method, so, when i use HTseq-count to gain read counts, for -s yes/no/reverse, which should i choose,and why
• 1,486 views
•
link
updated
by
Zhenyu Zhang
•
written
by
17318598206 •
•
written
by
17318598206 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Loss of strandedness in the Illumina Strandedness Total RNA protocol
written by Anjan
-
Tru Seq small RNA library prep kit
written by kb_93 •
-
Truseq Stranded Total RNA and NEBNext Ultra II Directional RNA library prep kit
written by deniz •
-
High no feature counts in ht-seq counts
written by eozcan •
-
Ovation RNA-seq system, bionfomatic alignment and htseq-count
written by nanoide
-
Salmon choosing library type
written by bharata1803
-
Defining transcript direction from sequencing
written by MarVi •
-
Detection of (novel) lnc-RNAs in 'normal' RNA-Seq data
written by aggregatibacter
-
Using htseq-count when a stranded library was assumed to be unstranded during tophat2 mapping
written by cajawe •
-
htseq-count using overlapping reads assembled with PEAR
written by t2
When in doubt, try all of them. Btw, since STAR aligner can generate STAR Count with all 3 options in one run, I don't see the benefit of using HTSeq.
so, how to use STAR to generate STAR Count with all 3 options in one run
It's by default and done together with alignment. Check this post RNA-seq: Explain STAR quantMode geneCounts values