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Hi again,
For Braker1, I had been providing BAM files produced by STAR.
Since you are now using StringTie assembly as part of the Braker pipeline, I was wondering if there are any notable perfo…
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I am using the script from Processing and integrating 5k PBMCs CITE-seq data to deal with my own data with totalSeq C, but the full pipeline fail when running the following step, the command and the e…
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Hi David,
I am trying super-deduper in some very very large datasets (like hundreds of millions reads). The reads have a random barcodes (unique molecule identifiers) in 5' and my goal is to collapse …
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Hello,
I have pulled the Docker Image and try to use the tool to characterize T cell receptor sequences in single-cell RNAseq data. It works fine on human data but for mouse samples I’m getting thi…
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Hi,
I am trying to run phaser using HiC data on a ~3 Mb region and ran into the "no alignment score value found" error.
**The command I am using:**
`python phaser.py --vcf ~/GT_myc_output.rec…
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Package the toil-vg pipeline into a docker container for submission to Dockstore.
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Hi, I used trinity(v2.8.5) to assemble the transcripts, but I always encountered the same **error** as follows:
-writing to Dir_SERVE_ERV.bam.minC1.gff/chrY/5/57191981_57208347.trinity.reads
CMD: …
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I was running the `tximport.r` code manually while trying to wrap my head around how it works and how it relates to the different types of salmon quant files and gene_count files generated by the pipe…
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Hello,
I am trying to visit https://cgwb.nci.nih.gov/cgi-bin/bambino but the connection times out.
I am also trying to download the jar via the following and the connection times out there as well.
…
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Using command `stub` blocks in Nextflow is useful when developing syntax and quickly testing pipelines. However, its use within nf-core is limited because the vast majority of nf-core modules do not h…
ewels updated
4 weeks ago