stringtie
stringtie copied to clipboard
gpertea
Transcript assembly and quantification for RNA-Seq
Hi, I was trying to extract count matrix by `prep.DE`, but I was getting the error. ``` Error: Text file with sample ID and path invalid () ``` This is...
Running Stringtie v2.1 produces up to 10-fold changes in FPKM values for the same samples in the same genes/locations when providing shortened versions of the same annotation file run in...
Hi, I was trying to to execute `prepDE.py `and I get the following error: Traceback (most recent call last): File "bin/prepDE.py", line 266, in transcript_len+=int(v[4])-int(v[3])+1 #because end coordinates are inclusive...
Hi, I'm interested in using StringTie finding novel last exons and the recently added `-ptf` option seems quite relevant. I have a couple of questions regarding recommended input sites and...
Hi, It is my first time with Stringtie v.1.3.4. Program has finished with no error. But in the gtf output folder a tmp folder still remains. Is that a problem...
The -i option reads: "keep merged transcripts with retained introns (default: these are not kept unless there is strong evidence for them)." I have several questions about how StringTie2 handles...
Hi, I am analyzing a dataset with several samples that I plan to use for downstream analysis of both gene level and transcript level analyses. I noticed an issue with...
Hi, I am reading your paper **Transcriptome assembly from long-read RNA-seq alignments with StringTie2**. In the section **Assemble of long RNA-seq reads**, it's mentioned that you correct potentially wrong splice...
Hi! I've been doing some tests with **1 transcript fully mapped by multi-hit/multi-mapped reads**, and found some issues with the -M parameter. - Using -M 1 (i.e., the default value)...
Hello! I have a question regarding the use of StringTie for assembly and merging of assembled annotations: I am working on a RNA-seq pipeline: I use HISAT2 for strand-specific alignment...
