stringtie
stringtie copied to clipboard
gpertea
Transcript assembly and quantification for RNA-Seq
Hello, When I use the -mix parameter, I consistently encounter an error message that says "Segmentation fault". Can you give me some advice? the parameters are the following: stringtie -o...
When I use the -mix parameter, I consistently encounter an error message that says "Segmentation fault (core dumped)." However, when I run StringTie separately with either short read BAM or...
GVec error
Hi, I'm having some trouble running Stringtie2 (v2.1.4) to assemble mapped isoseq subreads. I first trim adapters. `lima subreads.bam adapters.fasta subreads.bam` Convert .bam to .fastq `samtools fastq -@ 30 -0...
Whe I run /mnt/share/prog/stringtie-2.1.5/prepDE.py -i ./CIRI_sample.lst Error came as: sample file ./CIRI/1-2/1-2.gtf was not generated with -e option! Could you please tell me what's wrong and how to solve it?...
Hi there, thank you for the amazing tool. While assembling transcripts from ONT data, I noticed the canonical transcript of a gene of interest was missing and seems to be...
Hey, I have a question regarding StringTie --merge: I am using StringTie to assemble novel transcripts in a very small non model genome. The genome has very few introns and...
Hello, I am finding it hard to understand how Stringtie is constructing the transcripts using the RNA-Seq data. Here is the setup. I am mapping RNA-Seq reads from GenomeA onto...
Hello, I'm working on getting TPM from gene count file of star and checking whether the output is correct or not. I compared the correlation between tpm values of one...
**Warning: gene " TRNAK-UUU " (on NC_022272.1) has reference transcripts on both strands?** Hellow, I Googled and found out that this warning message comes out when there are both positive...
Hi Recently, I encountered some problem. I use the following code to get the bam file `hisat2 -p 46 -x ./1_index/99 --rna-strandness RF -1 ../0_archive/paired/${a}_R1.paired.fq.gz -2 ../0_archive/paired/${a}_R2.paired.fq.gz -S ./${a}.sam` `samtools...
