stringtie
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gpertea
Transcript assembly and quantification for RNA-Seq
Hi, I read about StringTie and I am wondering whether it could be used to de-novo assemble a transcriptome from RNA-Seq data using a genome of a closely related species...
I am working with stringtie/2.0.3 and have 2 questions regarding this tool. Q1: Is it better merge bam files first and then run stringtie or run stringtie for each sample...
Hi, I have CAGE-seq data, RNA-seq data and PacBio Iso-seq data derived from the same sample. I have been trying to find tools to build transcript models using these different...
Hello. We ran StringTie and then used prepDE3.py to get the gene counts and are seeing cases like the following where the gene id from the reference genome is mapped...
Hello, I was wondering if there is a way to find novel transcripts solely from the stringtie gtf file output? I was looking at the output and I found some...
Hello, I am using Stringtie2 quite frequently to assemble (annotate isoforms) some long-read cDNA data. One thing what I came a cross when I was looking at the results in...
hello, stringtiev2.1.7 there is my command: for i in *.bam ; do i=${i%.bam*}; stringtie -A gene_abund/${i}_gene_abund.tab -e -G ~/gtf/ensembl/Sus_scrofa.Sscrofa11.1.104.chr.gtf -o stringtie/${i}.gtf ${i}.bam & done and there are results: wc -l...
I have previously been using FLAIR for the so-called "hybrid" method. That program allows short-read data to correct long-read data. I wanted to test stringtie's new --mix method. Here is...
Hi, I have bam files aligned with STAR 2- PASS using the GENCODE fasta file and GENCODE annotation file. Then I want to assemble transcripts using the Refseq annotiation because...
Hi Geo, In my BAM file, there is a certain number of spliced read alignments which do not have the XS tag. My understanding is StringTie will ignore those spliced...
