stringtie
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gpertea
Transcript assembly and quantification for RNA-Seq
Hi I used stringtie to assemble a new transcriptome and merge with a reference one. The output gtf has ~30 lines without strand info in field 7 , compared to...
Dear, I need to convert MSTRG.number into Gene name or Gene Symbol to be able to run on an R script that allows me to perform differential gene expression analyzes....
Hi, I am having trouble with geneIDs in gene_count_matrix file. I will give an example: This transcript MSTRG.43175 found twice in the matrix. And they do not have the same...
Hi, I'm running stringtie as part of the [nf-core rna-seq pipeline](https://github.com/nf-core/rnaseq) with bacterial transcripts and [this reference](https://www.ncbi.nlm.nih.gov/genome/152?genome_assembly_id=154382). Many samples finish successfully, but several throw errors at the `stringtieFPKM` step. These...
I am running STAR and StringTie on RNAseq data from 4 samples (PE 100bp, 60M reads/sample, stranded) and am looking at the merged.stats file. The numbers for novel stuff being...
According to the manual, the "-m" option controls the minimum length allowed for the predicted transcripts. So, I expect that the output gtf file will just contain transcripts longer than...
One of my sample may get something error. When I run stringtie with these data, it behaves very high memory consumption, even touch to 600G. In fact, this bam file...
Hi, I'm ran stringtie v2.1.4 and it stopped writing to tmp folder after the .gtf.tmp reached a very specific size (209911808-B). I haven't had any issues with other BAM files...
I've noticed some transcripts have negative coverage values in the output gtf file from StringTie 2.1.3b. Can this be a bug? Below is my script. ``` while read bam do...
Hi, we are finding this error during a merging of three different gtfs that were generated with psiclass. I know psiclass is not your program, but could you take a...
