stringtie
stringtie copied to clipboard
gpertea
Transcript assembly and quantification for RNA-Seq
hello I use stringtie v2.2.3 to obtain counts data of transcriptome for downstream difference analysis. This is my stringtie Code: `stringtie -p 8 -o "$spath/$id.gtf" -l $id -G $gtf -B...
Hello, I am using stringtie for long-read ONT data and I came across an issue with transcript ends being trimmed not enough, although a drop in coverage is clearly visible....
I am using StringTie v3.0.0 to discover novel transcripts from short-read RNA-seq data. After quantification, I noticed that some transcripts/exons have a coverage (cov) of 0, even though reads are...
Hello StringTie team, I'm running into an issue where certain transcripts present in my BAM files are not appearing in the GTF output from StringTie. This causes errors when I...
I am attempting to use prepDE.py to prepare my stringtie output for DEseq2. My stringtie command is as follows: `stringtie -e -G Gmax_275_Wm82.a2.v1.gene.gff3 -o ${name}.gtf ${bam}`. My prepDE.py command is...
Hi @gpertea @smoe I used the above command to merge two GTF files, which were constructed by PacBio to represent full-length isoforms `stringtie --merge -G Ref_gene.gtf -o Gb.gtf final.gtf ML.filtered.gtf`...
Dear stringtie team, I am using stringtie to quantify RNA-Seq data for 104 samples from 7 green algae strains. the problem is that in the first round of stringtie aligning...
Hi! Thanks for the great tool, and continued updates over the years. I noticed that the manual does not mention the effect of `--rf` when using `--mix`. Does the `--rf`...
Would you like to add more error handling for return values from functions like the following? * [fclose](https://pubs.opengroup.org/onlinepubs/9699919799/functions/fclose.html "Close a stream.") ⇒ [TInputFiles::start](https://github.com/gpertea/stringtie/blob/b4366c542af25f9f25e37c434858718d2f757b3c/tmerge.cpp#L119) * [fputs](https://pubs.opengroup.org/onlinepubs/9699919799/functions/fputs.html "Put a string on a...
Would you like to [wrap any member pointers](https://github.com/gpertea/stringtie/blob/b4366c542af25f9f25e37c434858718d2f757b3c/SuperReads_RNA/global-1/quorum/src/mer_database.hpp#L65-L92 "Update candidate: hash_with_quality class") with the class template “[std::unique_ptr](https://en.wikipedia.org/wiki/Smart_pointer#unique_ptr "Description for the usage of smart pointers")”?