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etal / cnvkit

Copy number variant detection from targeted DNA sequencing
http://cnvkit.readthedocs.org
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Can I use output of featurecounts output to replace the input of import-rna? #627

Closed deb0612 closed 3 years ago

deb0612 commented 3 years ago

Dear sir, I had problem to get the RSEM produces. Should I use other programs to get the input of import-rna ?

tetedange13 commented 3 years ago

Hi @deb0612 ,

Not an author of CNVkit + not an expert in RNA data/tools => However it is said in CNVkit's documentation:

  • Gene counts: Alternatively, the gene Ensembl IDs and per-gene read counts can be read from a simple 2-column, tab-delimited file. This format is used by TCGA level 2 RNA expression data. You can also create the equivalent on your own from the output of another RNA quantification tool like Salmon or Kallisto.

Is it not what you want? => In other words, try to transform featureCounts's output, to obtain a simple 2-column tab-delimited file with your by-gene counts? (cannot help you on this, sorry...)

Hope this helps. Have a nice day. Felix.

tskir commented 3 years ago

Hi @deb0612,

What @tetedange13 says is correct, however, import-rna should also support RSEM output. Could you share some more details about your workflow please, e.g. which parameters you're running import-rna with?

tskir commented 3 years ago

Hi @deb0612, just wanted to check in with you to see if this issue is still relevant. If so, could you please provide the parameters you're running import-rna with?