-
```
What steps will reproduce the problem?
1. runing star with parameters:
star --genomeDir $GENOME_DIR \
--readFilesIn $READS1 $READS2 \
--runThreadN $TREADS \
--genomeLoad LoadAndKeep \
--alignInt…
-
Hello
I'm use R 3.5.1. I got the GDC data-molecular data-hamornized database(hg38)-Project KIRC-Transcriptome Profiling-Gene Expression Quanlification-HTSeq FPKM UQ-Primary solid tumor and download s…
-
```
What steps will reproduce the problem?
1. runing star with parameters:
star --genomeDir $GENOME_DIR \
--readFilesIn $READS1 $READS2 \
--runThreadN $TREADS \
--genomeLoad LoadAndKeep \
--alignInt…
-
I have been using hisat2-stringtie-DESeq2 pipeline for a while, and then I realized the sum of raw counts from all the genes only accounts for 20% of my mapped reads. That is a pretty low number and t…
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Hi @jaudoux
I am wondering how gene-counts.tsv.gz, transcript-counts.tsv.gz are being generated, Are they raw-counts, or using a feature counting tool?
In my opinion, it would be so handy if the…
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1) add a tool to verify strandedness for RNAseq:
https://github.com/betsig/how_are_we_stranded_here
2) Add gene/transcript expression comparison/correlation between stringtie and kallisto
3) ut…
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We need to dynamically create a dependency graph based on the input and output files to visualize the progress of the workflows.
Some options we should consider from snakemake
--d3dag, --dag, --ru…
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The pipeline seems to be working, but I don't get the same output.
I used the sMETASeq_NEXTFlex.sh for D12_S12_R1.fastq file only (due to limited space on my laptop). My commands look like this (I…
-
**Software versions**
- `HTSeq` 2.0.1
- `Python` 3.9.2
- operating system Ubuntu 18.04
**Describe the bug**
I was trying to use the in operator to determine whether any values were set in a spe…
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I installed R-3.4.1 by Miniconda, and managed to installed the GDCRNATools, but while testing with your instruction to download RNA data (http://bioconductor.org/packages/devel/bioc/vignettes/GDCRNAT…