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gpertea
Transcript assembly and quantification for RNA-Seq
I am trying to assemble four relatively small bam files and getting a segmentation fault: 11 error. I can assemble two of them but the other two give this error....
Hi I was preparing the count of string tie for DEseq2 analysis by prepDE.py and when I enter > prepDE.py -i all_gtf_3.txt -v it turned out to be an error...
Hi, are there any general recommendations for calling StringTie to assemble transcriptomes using RNA-seq data from small-genome organisms such as _S. cerevisiae_ and other fungi? That is, adjusting certain parameters...
I input an unpublished reference assembly to stringtie with the -G option . The reference gtf has no UTR data; the transcript boundaries in every case are coterminous with the...
New transcripts appear after merging the illumina and pacbio data of multiple organizations using stringtie2 --merge。At first, we only need short transcripts, and new longer transcripts will appear after merging。
Hello, I'm using Stringtie v2.0.4 for my RNAseq data analysis. I have a reference genome and annotation file but I still intend to identify novel genes since the annotation is...
This issue is reproducible on the last test example: ``` stringtie --mix -e -G mix_guides.gff -o mix_e.out.gtf mix_short.bam mix_long.bam ``` The output file has only 11 transcripts instead of the...
Hi, I'm using stringtie to assemble a transcriptome using a reference annotation made with a predict annotation containing only CDS regions. This is the command line I'm using: ``` stringtie...
Dear gpertea and all Stringtie maintainer, I performed single sample assembly with StringTie however the reconstructed 5 end is incorrect even the read coverage support in bigwig is obvious. The...
Hello, In the Stringtie2 paper, it is briefly mentioned that --mix mode uses short reads for the splice junction correction. So, I as wondering in the output gtf file generated...
