User: gnomee

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gnomee20
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5 hours ago
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2 months, 1 week ago
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c******@dkfz-heidelberg.de

Posts by gnomee

<prev • 7 results • page 1 of 1 • next >
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Comment: C: STAR alignment EXITING because of FATAL ERROR: could not create output file
... The `touch` command worked, which was what puzzled me in he first place. ...
written 5 weeks ago by gnomee20
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Comment: C: STAR alignment EXITING because of FATAL ERROR: could not create output file
... This solved it! I changed the `--outFileNamePrefix` to `/home/c479e/ANTCoN_analysis/STAR/65312-RNA-FFPE/` as you suggested, and now it runs fine. I thought it was also possible to specify the first bit of the file name with `--outFileNamePrefix`. The R2 was a spelling error in the post, it is correc ...
written 5 weeks ago by gnomee20
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STAR alignment EXITING because of FATAL ERROR: could not create output file
... I am trying to align RNA-Seq data using STAR. However, STAR does not start the alignment, but exits with the following error: EXITING because of FATAL ERROR: could not create output file: /home/c479e/ANTCoN_analysis/STAR/65312-RNA-FFPE_L001_Log.out Check if the path /home/c479e/ANTCoN_an ...
star rna-seq written 5 weeks ago by gnomee20 • updated 5 weeks ago by caggtaagtat930
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Monovar with single BAM file
... I am trying to do SNV calling with single cell data. For this, I wanted to apply Monovar to the data that I previously aligned using cellranger. Is there a way to use Monovar without splitting the cellranger BAM output file into BAMs for each individual cell, so instead just using the original BAM w ...
snp single cell written 6 weeks ago by gnomee20
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Answer: A: Cellranger count fails at mapping
... I think I solved the issue now. I realized that the directory specified in `--fastqs` only contained symlinks to the acutal fastq files, which cellranger apparently could not handle. Why it failed only at that specific step I do not know, but it runs smoothly now that I specified the correct directo ...
written 9 weeks ago by gnomee20
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Comment: C: Cellranger count fails at mapping
... I rerun it with the latest cellranger version (3.1.0) now, however this results in the same error. ...
written 9 weeks ago by gnomee20
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Cellranger count fails at mapping
... Hi all, I am fairly new to scRNA-Seq. I am trying to align 10X datasets using cellranger. However, cellranger fails at the mapping step during chemistry detection, and I do not understand why. This is my code: cellranger count --id=4CHH4R_tumor1 \ --fastqs=data/K46R-4CHH4R/tumor1-h01 \ - ...
alignment rna-seq written 9 weeks ago by gnomee20

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Scholar 9 weeks ago, created an answer that has been accepted. For A: Cellranger count fails at mapping

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