Benedek Dankó

Generated html file empty

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Hello, I have done the following steps: 1. extract sites: ``` for f in "$@"; do LOC="/disk/work/shared/data/MDS/${f}/alignment/STAR" cd ${LOC} for bam in *_Aligned.out_sorted_rg.bam; do base=$(basename $bam .bam); ${SOMALIER} extract -d...

Hello, I arm trying to use the ```r TCGAbiolinks:::getProjectSummary("TCGA-HNSC") ``` command, but I get the following message: ``` Error in curl::curl_fetch_memory(url, handle = handle) : Timeout was reached: [api.gdc.cancer.gov] Resolving...

Error during quantification of FASTQ files

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Hello, I generated the Whippet index file: ``` julia bin/whippet-index.jl --fasta data/genomes/fasta/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz --gtf data/transcriptomes/gencode/gencode.v34/gencode.v34.annotation.gtf.gz --index data/whippet_index ``` And then approached to run the quantification: ``` julia /home/bd1/tools/Whippet.jl/bin/whippet-quant.jl /home/bd1/mds-datasets-no-backup/dataset2/fastq/SRR6781235_1.fastq.gz /home/bd1/mds-datasets-no-backup/dataset2/fastq/SRR6781235_2.fastq.gz -x...

[This line](https://github.com/BioinformaticsFMRP/TCGAbiolinks/blob/e78993d11ca7ea3259b4ba2fba94f22bd2b2d4c5/R/analyze.R#L864C5-L872C6) in the `analyze.R` code leads to the following error if you don't set metadata to FALSE and if your samples have different sample IDs: ```r Error in names(x)