STAR-SEQR

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Hey! I have to detect fusion transcripts on single-end reads using star seqr. However, I always get an error message "starseqr.py: error: the following arguments are required: -2/--fastq2". I just...

suhana13

Error: no SAMPLE.Chimeric.out.junction file

3

When trying to run STAR-SEQR, I get this error after STAR has finished alignment: `OSError: [Errno 2] No such file or directory: '/path/to/SAMPLE.Chimeric.out.junction'` The reported STAR command line specifies "--chimOutType...

personalis

Hi, I was wondering if you had a literature citation we should use for STAR-SEQR? many thanks!

brianjohnhaas

The latest networkx2.1rc1 version renames several functions. Specifically: ``` adj_mat = nx.to_pandas_dataframe(node_graph) AttributeError: 'module' object has no attribute 'to_pandas_dataframe' ``` The function is now called `to_pandas_adjacency` per: https://github.com/networkx/networkx/pull/2811 Either specify...

jasper1918

Potential future issue

1

/pandas/core/groupby.py:3961: FutureWarning: using a dict with renaming is deprecated and will be removed in a future version return super(DataFrameGroupBy, self).aggregate(arg, *args, **kwargs)

jasper1918

STAR alignment not working

1

I am running STAR-SEQR from the fastqs and getting this error: ``` 2023-01-31 22:26 - ERROR - EXITING because of fatal PARAMETER error: --outSAMattributes contains ch tag, which requires BAM...

anoronh4

System Info: ``` STAR-SEQR version= 0.6.7 Docker version (Server/client): 20.10.12 OS: Ubuntu 20.04.5 LTS x86_64 ``` I'm running star-seqr via the docker image: `eagenomics/starseqr (Image ID: 0e715fd07246)` First I generated...

ReWeda