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Hi,
I would like to use htseq-transcriptome on some bam files that were generated using RSEM with a de novo transcriptome as a reference. Therefore, I don't have a GTF file. So, I am wondering how…
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Pipeline should output an ExpressionSet (in addition to a tab-delimited expression matrix) for each of the counting outputs (stringty, HTseq, FeatureCount, ...)
Look at Hydra code for examples
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Hi Nuno,
I was wondering, is there any reason why TPM values are rounded to 2 decimals? In some experiments I see over 20% of genes
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I have successful instal using bioconda using htseq-count. I have this error.
```
(rna_test2) [riva@ilmn-qm ~]$ htseq-count -h
Traceback (most recent call last):
File "/home/riva/miniconda2/en…
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Hi Colins,
looks really good!. Some feedback
1. I think we need to describe the problem domain as in what problem this tool is helping solve and how is it doing it (uses manifest to download the f…
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Here the error:
```
type == 'gene_expression' &
+ analysis.workflow_type == 'HTSeq - Counts')
> manifest_df = qfiles %>% manifest(…
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Hello,
Would it be possible to auto-adjust the amount of memory used by the process based on the input file size?
Thank you!
Olga
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I used HTSeq in Linux,Now I need it in my windows but the modules give this error when I tried to download it.
os.symlink(py_fdn+fdn, fdn)
AttributeError: 'module' object has no attribute 'symli…
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Hi,
I try to run htseq-count from my MacOs. I am using python3.6. When I type the command line
htseq-count --stranded=no file.bam file.gft
hstseq starts the run and after processing the gtf file,…
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In order to test if the latest conda version is actually working for us right now, I started to test all IUC tools against latest miniconda3.
```
% /home/bag/miniconda3/bin/conda --version …