stringtie
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gpertea
Transcript assembly and quantification for RNA-Seq
The mix option takes as input short-read data and long-read data. However, in my case, I have both PacBio and Nanopore data. The mix option does not allow 3 inputs....
Hello! I am using nanopore RNA-seq to compare gene expression. For some genes, my data set only have partially transcribed transcripts which lack reference_id attribute in StringTie's output record, but...
Hi, I don't understand the FPKM filter used by stringtie --merge (version 2) to remove transcripts with low abundance. I got an individual assembly for each sample (28 samples) using...
Currently, when you have dynamic libraries in your `LD_LIBRARY_PATH` and try to build `StringTie` you will get an error like below, because the `Makefile` of `HTSlib` picks them up and...
Hi, As per the published hisat2/stringtie protocol, hisat2 is used with paired-end reads. I was wondering if hisat2 can be run using paired-end and singleton/single-read files together using -1, -2...
Would it be possible to get raw read counts directly from Stringtie, instead of coverage values to transform with prepDE.py? I understand prepDE.py uses a formula that gives an estimate...
Hi, there! I have used the stringtie2 to the genome-based transcripts assembly. I used the hisat2 to do the alignment of the RNA-seq data , and then the picard the...
Hi, thank you for this wonderful tool and detailed explanation. I've noticed that from the below release, ------------ 4/21/2020 - v2.1.2 release new features to improve transcriptome assembly: introduced an...
Hi, I'm trying to run StringTie for transcriptome assembly using BAM files generated by 'STAR' The command line that I used is followed ``` stringtie sample1.sorted.bam -f 0.1 -c 2.5...
Hi I am trying to run StringTie for hifi isoseq reads (ccs fastq reads) by first running the deSALT aligner with '--trans-strand' option and then provide generated sort bam to...
