stringtie
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gpertea
Transcript assembly and quantification for RNA-Seq
In order to confirm the error of the splicing function due to the mutation, it is necessary to check the existence of the intron. I wanted to quantify the intron...
I have mapped data using STAR and know trying to generate assembly using stringtie, the reference annotation gtf file contains [38464 genes and 47387 transcripts](https://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Pteropus_alecto/all_assembly_versions/GCF_000325575.1_ASM32557v1/GCF_000325575.1_ASM32557v1_genomic.gtf.gz). When I tried to assemble...
Hi, I want to quantify transcript abundance for ONT DRS data, can I use the TPM value from the gtf?  Or I should use other software to quantify? And...
Hello ! I have a question about an interpretation done by stringtie, using Nanopore datas. I generated my bam files with `minimap2` and used them as input of stringtie without...
Hi, stringtie(v2.2.1) Segmentation Fault when I used it to merge scallop2, why? stringtie --merge -o scallop2.merge.gtf scallop2.list gtfs I used have been sent to [[email protected]](mailto:[email protected]). Best, Kun
Hi, I am using the latest version (2.2) of Stringtie and while using the expression estimation mode (-e) I lost ~1k transcripts compared to the denovo assembled GTF file. Also,...
After re-estimating my transcripts using stringtiemerge with -eB option, I want to do differential expression analysis at the gene level. For that, I tried Ballgown as well as DESeq2 (after...
I merged 93 samples with StringTie merge. Most of the isoforms were merged well, but when there is another isoform with another exon on the 5' side (in the example...
Thanks for developing the tool! After running the superreads.pl, the LongReads.fq file is empty. But in work1 directory, the superReadSequences.fasta file looks like some assembled superreads. I wonder what the...
Hello, I don't know what went wrong, could you tell me? thank you
