stringtie
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gpertea
Transcript assembly and quantification for RNA-Seq
Hello, and thanks for StringTie! Due to what seems to be a copy-paste error that checks the wrong variable, setting -s always fails. ~~Also, there's an ominous comment about `//...
Dear maintainers, There are some building warnings and This PR is to removing these warnings Could U please review? Thanks
Hi, I am using StringTie (v2.0.3) to search for novel lncRNA transcripts. After running stringtie on my on individual samples, I use --merge to merge samples into a single gtf...
Hello, I would like to know how the coverage in the output file is calculated? And is the ```--merge -c``` parameter simply filtering out transcripts with unqualified coverage in each...
Hi all, I would like to use both long read (isoseq) data and paired-end RNA-seq (Illumina) data to produce gene assemblies. what would be the recommended way to do this?...
Hi, I met the similar problem when I use stringtie: "Error: the input alignment file is not sorted! Alignments (965520) already found for chr1_1 !". I was working with the...
Upon checking the gene.csv file generated after running prepDE.py3, the bottom row contained a row "  does it have any implications? also, the trans.csv seems incomplete...
I get the following error when running prepDE.py on stringtie estimate output: ``` Traceback (most recent call last): File "./prepDE.py", line 255, in geneDict.setdefault(geneIDs[i],{}) #gene_id KeyError: 'STRG.337.1' ``` I only...
Hello, I am interested to compare and plot novel transcripts identified by stringtie (guided). Will the novel transcripts be included in ballgown file? If not, what other tools can be...
I wonder 'else' clause (at l.172-173 of version v2.2.1 Latest on Jan 26, 2022) should be commented out (or deleted) in the block of badGenes check in `prepDE.py3`. ``` for...
