stringtie
stringtie copied to clipboard
gpertea
Transcript assembly and quantification for RNA-Seq
Thanks for developing this amazing tool ! I recently used stingtie to assembly the transcripts of tumor samples and gained some transcripts. But they didn't contain the junctions I extracted...
Hi, I am wondering if stringtie can process chimeric reads (eg. multiple subsections of that read align to different positions in a reference genome). Best, YM
Hello, I was wondering if you could clarify how best to deal with non-canonical splice sites when assembling long-read ONT data, please. My organism uses a wide range of splice...
I used stringtie to analyse the output of my hisat alignment in >30 human samples in parallel and detected single samples with FPKM values of 0 for several genes although...
i was trying to get transcript file using stringtie then error occured stringtie output_sorted_bam -o transcripts_gtf -G Piper_nigrum.gff3 -A assembly.txt WARNING: no reference transcripts were found for the genomic sequences...
Hello! I am getting the following error for stringtie command: stringtie -o outputfile -G annotationfile bamfile "Error: no valid ID found for GFF record Aborted (core dumped)" I am using...
I'm trying to understand if I can use stringtie with some RNA-seq datasets I received from a collaborator. The reads are paired-end, which is different from the previous times I...
I'm running the epi2me oxford nanopore single cell analysis pipeline and get this stringtie error: Caused by: Process pipeline:process_bams:stringtie (1) terminated with an error exit status (1) Command executed: Add...
Currently, stringtie does not support gzip'd GTF input. The error: ```console Warning: unexpected tab character in last column, line truncated: �O�+���9��2��e�Ih6B2�s����K��wJ�*� ��ܟ� ``` It would be helpful if gzip (and...
Hello, I'm using stringtie:2.2.2 to assemble transcripts by --mix model. All samples were finished successfully except one sample. and I separated the bam file by chromosome to check the bam...
