STAR-SEQR

STAR-SEQR copied to clipboard

https://github.com/ExpressionAnalysis/STAR-SEQR/blob/8889bc879c647c2174c37ee4a69a27626814c22b/starseqr.py#L443-L446 I'm trying to use a pre-aligned bam and it errors here because it looks for sam file that doesn't exist. I believe this is a mistake. Do I need...

arichards2564

Hello! I've been trying to run STARSEQR with reads already aligned (with options for arriba, star-fusion and STARSEQR). When running with the following options: `starseqr.py -sb -sj -p -t 8...

GACGAMA

nested renamer is not supported

2

Hi I am running starseqr on my samples and stuck in error. starseqr.py -1 sample_1.fastq.gz -2 sample_2.fastq.gz -m 1 -p starseqr_test -t 50 -i STAR_FUSION_LIB/ref_genome.fa.star.idx/ -g genomic.gtf -r genomic.fa -vv...

Ajeet1699

Runtime far exceeding Wiki-suggested runtime

2

Hi there, I've been trying to use this software to analyze single-cell RNA-seq data. I was able to successfully run the STAR Index generation, and starseqr.py does not appear to...

dstueckm

Running the following command generates an error: `starseqr.py -1 26-R-EMEA1-VA_S8_trim_L001_R1_001.fastq.gz -2 26-R-EMEA1-VA_S8_trim_L001_R2_001.fastq.gz -m 0 -p ./ -t 25 -i ./ -g ../genomes/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf -r ../genomes/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa` ``` 2021-04-18 20:45 - ERROR -...

kate-simonova

If anyone comes across this error: "AttributeError: 'IntervalTree' object has no attribute 'search'" try downgrading your version of intervaltree to version 2.1.0. Intervaltree version 3 was released in late 2018,...

kskuchin

read Chimeric.out.junction ERROR，about pandas

1

Dec 05 09:41:16 ..... loading genome Dec 05 09:42:08 ..... started mapping Dec 05 09:53:04 ..... finished mapping Dec 05 09:53:04 ..... finished successfully 2020-12-05 09:53 - INFO - STAR...

ruizgo

IOERRROR in docker

1

I am running using the latest cwl, however am getting the error below. I tried updating the docker container but this did not make a change. ``` [48006 rows x...

medcelerate

exact tool version .yaml available?

1

Hi, it seems that STAR-SEQR might no longer be useable with most recent versions of its dependencies. I have installed it via bioconda as per the following website, and keep...

mapostolides

Salmon quant

2

As is, starseqr always requires fatqs even if a STAR alignment is provided. If we modify the salmon call to do alignment mode in this scenario we can bypass the...

jasper1918