StringTie error: list index out of range

Dear all,

I am trying to run StringTie on a aligned RNASeq data.

However it ends with this error:

"Fatal error: Exit code 1 () Traceback (most recent call last): File "/galaxy/main/deps/_conda/envs/__stringtie@1.3.3/bin/prepDE.py", line 171, in <module> if v[2]=="transcript": IndexError: list index out of range"

Can anybody suggest any solution?

Looking forward your helps

Nazanin Hosseinkhan

stringtie error galaxy

• 2,288 views • link

written 8.5 years ago by nazaninhoseinkhan

Could you please add the command you're trying to run?

• 0 views • link

written 8.5 years ago by Philipp Bayer

1 answer

Hi, I am using StringTie in Galaxy server.

• 0 views • link

written 8.5 years ago by nazaninhoseinkhan

I hope someone knows the answer kissanime

• 0 views • link

written 8.5 years ago by jennietodd141 •

More posts like this

RagTag patch error--"tuple index out of range"
written 3.5 years ago by schmiggle •

I'm trying to correct a long-read assembly with a short-read scaffold; I'm hoping to fill in the short gaps in the scaffold with the matching …
error in anvi'o tool
written 5.4 years ago by Kumar

I have installed `anvi'o` in my miniconda3 (Ubuntu 18.04 LTS) laptop computer and successfully executed `anvi-self-test`. I intended to execute `anvi-setup-ncbi-cogs` to annotate my contigs, …
blast2gff IndexError: list index out of range
written 6.0 years ago by Begonia_pavonina •

Hello everyone, I have an issue with the mgkit tool: blast2gff. I am trying to output a GFF file from a BLAST result (with the …
From StringTie to DESeq2
written 7.4 years ago by Morris_Chair

Dear all, After generating bunch of files with stringTie command line, I want to use DESeq2 for differential expression analysis. I understand that I have …
Deeptool ComputeGCBias causes fatal error
written 7.6 years ago by mfro1505 •

Hi together! I tried to use the deeptool ComputeGCBias with a sorted BAM file as Input. I used a BAM file directly from BWA mapping, …
deepTools2: compute matrix error
written 7.9 years ago by dabates06 •

I get this error when trying to use computeMatrix in the DeepTools2 suite: Fatal error: Exit code 1 () Traceback (most recent call last): File …
kover learn issue
written 8.0 years ago by alhicks32188 •

Hi, I have run kover (http://aldro61.github.io/kover/) successfully previously, but in attempting to run in on a new dataset, I was able to create the dataset …
igv_plotter error, I cannot run igv_plotter on my BAM file, RuntimeError: Xvfb did not start
written 9.1 years ago by biomagician

Hi there, I have installed igv_plotter with sudo pip install igv_plotter and checked it with igv_plotter igv_plotter usage: igv_plotter [-h] [-o OUTPUT] [-L LOCUS_FILE] [-v] …
Fastqc 0.67 errors while Fastqc 0.64 does not
written 9.6 years ago by rjames •

When I run FastQC version 0.64 on a fastqsanger dataset I get results. However when I run FastQC version0.67 on the same dataset I get …
How to extract sequence from fasta file with specific coordinates?
written 10.2 years ago by tcf.hcdg

I would like to extract sequence with specific coordinate. I did the blast search and now from this output I need to extract the 100bp …