15 results in 0.0022 seconds.
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Stringtie product is in fastq format...
I first used hisat2 and successfully align the SRA sequence to the reference genome, then used stringtie for the annotation. The script is as follow:... -
Extracting gene sequences from Stringtie assembly
Hi all,
Forgive me if this question has been posted before (I'm new to this forum). In the past, when doing transcript-level RNA-seq analyses,... -
gff2gbSmall
Hi, everyone.
I am in trouble converting gff format file to genbank format.
The gff format file looks like:
Scaffold_15;HRSCAF=18|... -
StringTie merge- can someone help me understand its output?
Hello,
I am currently using StringTie merge on a StringTie output in order to discover genes that are not already in my reference annotation.... -
stringtie error: GFF not recognized
Hello,
I'm trying to run stringtie with a reference genome, and I'm getting the following error:
WARNING: no reference transcripts... -
Adding Blastx Hits to un-identified genes in StringTie Output
Hi all,
I've been using a general pipeline of Hisat2 -> StringTie -> Ballgown for differential gene expression analysis in a non-model... -
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... -
Issue with StringTie--not picking up reference gene IDs
Hello, I am using StringTie for RNA-seq analysis and want to use DESeq for differential gene expression analysis.
After running the command... -
String - possible to ignore alignment for custom chr signatures
I am working on pdx model and used a hybrid genome to make my alignments. I tagged all the chr of mouse genome as mm10_* i.e. mm10_chr1, mm10_chr2 etc..... -
StringTie - isoforms not overlapping
Hi,
I am using StringTie for transcriptome reconstruction and identification of new isoforms.
While I was exploring the "[file]-transcripts.gtf"...Last edited by pbarros; 04-26-2017, 03:22 AM. -
stringtie genes abundances bug or problems?
Hi, I am using stringtie-1.3.2d.Linux_x86_64 to caculate genes abundances with -A parameter.
However, some records seems not so good.
... -
Stringtie is breaking up an annotated gene
Hi,
I'm pretty new to RNA-seq analysis. I was able to map RNA-seq data with HISAT2, and am now trying to use Stringtie for the FPKM quantitations.... -
stringtie parameters
Hi,
I have been trying to use Stringtie for transcriptome re-assembly, based on a reference gtf file.
Here is how I ran it:
... -
StringTie Output
Hello all,
I am an RNA-Seq newbie who is having some issues with the StringTie output. I am currently using StringTie on Galaxy with the... -
stringtie output has exons instead of transcript annotation
Hi,
has anyone used stringtie program? I have a genome annotation that mostly has one isoform annotated per gene. I tried to use stringtie...
