Using StringTie with CAGE-seq data
Hi, I am currently reading a paper (Figure 3b) where they use CAGE-seq data as an input for StringTie, to assemble isoforms.
I am very confused how this is possible, since I thought that only produces very short reads (~30bp) at the 5' end of our mRNA. I understand how StringTie works with RNAseq data, but I have no idea how it works with Cage-seq because of the short reads which should be located manily at the 5'end.
Am I missing something obvious? Or can somebody explain to me how it works.
Any help is much appreciated!
Thanks
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Plant transcriptome analysis and annotation
written by martta95 •
-
Stringtie coverage calculation for DE analysis
written by Tihana •
-
how to removed the first two nucleotides from a fastq file (single-end)
written by 17318598206 •
-
conceptual question about paired end sequencing
written by nhaus •
-
RNA-seq transcript assembly, novel transcript identification and visualisation
written by andreismolnikov00 •
-
StringTie - Multimapped reads
written by sneha108.ss •
-
Are TPM values generated by different programs comparable?
written by amy.bashir
-
How to analyze CAGE-Seq data?
written by heir_of_isildur88 •
-
How to trim illumina reads for poly-A tail and mini-exon presence
written by Buffo
-
CAGE processing (from BAM to expression values per Gene/Isoform)
written by Tobias
They assembled unannotated TSSs, not whole isoforms.
Could you elaborate what you mean? I only see two Cage signales, one in Intron 1 and around exon 2. Yet they predicted Isoforms with many more exons
Check which version of CAGE was used to sequence the data. Newer versions of CAGE (deepCAGE, nAnT-iCAGE, etc.) can have bigger inserts and be sequenced in paired ends, so you can get more coverage of the fragment.