stringtie
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gpertea
Transcript assembly and quantification for RNA-Seq
I've tried to compile jellyfish and quorum. But it didn't work. So, I downloaded all packages from github specific directories and compiled everything. In the end, a error message for...
I do not see a cpp file named release.cpp, which may explain why there is a failure on `make release` during installation. Maybe I'm missing something though!
Hello! I am using v2.2.1 but encounter a similar error. ``` CH_RNA-ZF_BPATCS/CH/EC_output$ prepDE.py -i sequence_mapping.txt -g genematrix.csv -t transcriptmatrix.csv Error: could not locate transcript gene-b0731 entry for sample Chl1-2 Traceback...
Hi there, I am trying to use a reference guided annotation assembly for Stringtie. The gtf file is self made, and the bam files contain the fastq files. I use...
So I 'collapsed' some long read data into a gtf with : `/home/apps/stringtie2.1.4/stringtie ${BAMLIST} -p ${THREADS} -L -R -o hg38_merged.gtf` I then try to quantify each sample/bam against this cleaned...
HI,gpertea. Histat2 can add XS tag for all read alignments,I have a stranded library (fr-firststrand) data, I use STAR to mapping genome and set options --outSAMstrandField intronMotif which can add...
I have close to 21 samples and all of them are giving me a segmentation error message. I ran one of them in -v mode, and here is what I...
Hi, I am trying to assemble RNA-seq data for gene annotation using StringTie. But the program fails returned the "Segmentation fault" error. The program stop at the Chr1:17731527-19123574 site as...
During the bam-gtf conversion step, I set the -c 3 parameter, but when I checked the generated gtf file, I found that there were still transcripts with cov values less...
Hi, I am using both short- and long-read-based BAM files in StringTie. However, the '-mix' mode resulted in an error message of 'Segmentation fault' as attached below. I have tried...
