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Just wondering whether different kinds of input measures will affect the results? It is stated in the manual that "Estimates of gene expression are typically obtained using RSEM, HTSeq, Cufflinks, Sal…
zji90 updated
6 years ago
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Doing this already with the REST API using the htseq API from BROAD:
- [ ] project mismatches correctly as subfeatures (or correclty populate another string?)
- [ ] handle MD string mismatches cor…
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I am trying to download RNA-seq data. The actual download works:
```
gdc_query = GDCquery(project = "TCGA-LUAD",
data.category = "Transcriptome Profiling",
data.type = "Gene Expression Quantificat…
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Prioritize some now that fail on the default cluster?
I am not sure if these dispatch to Jetstream/Roundup depending on job scheduling (meaning a re-run could start up on Jetstream, even if it takes …
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Hi,
This is my htseq-count command:
```
htseq-count -f bam \
-r name -s yes \
-a 10 -t exon -i exon_id \
-m union \
sample_Aligned.out.bam gencode.v23.annotation_subset.gff > sample_Aligne…
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Hi there,
This is a question more than an issue. I've built a transcriptome using the PASA methodology (dnv assembly + reference assembly + PASA pipeline) using both control + condition samples tog…
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Updated the current version using
`devtools::install_github(repo = "BioinformaticsFMRP/TCGAbiolinks")`
The following error occurs with TCGAanalyze_SurvivalKM
```
solve.default(vv, temp2) :
Lap…
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Hi,
I have a bunch of samples from various tumor types in which I want to get the exon level expression of the gene IDO1. My aim is not to do any differential expression of any sort because there a…
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Hi,
I am not able to get any output from MultiQC due to it ignoring my fastq files in the directory. Here is the command I ran and the output I got form the verbose mode:
```
[kumara22@login1 t…
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Hello,
while building htsqe-0.9.1 from release archive (https://github.com/simon-anders/htseq/archive/release_0.9.1.tar.gz)
make doc, aka make html was giving the following error message
``…