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Recent Replies
Comment: STAR is running but .sam file size does not increase after hours mapping
by
GenoMax
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Memory =/= disk storage.
Likely you will need to diagnose this yourself since we don't have access to your data/server. Your command obvio…
Comment: STAR is running but .sam file size does not increase after hours mapping
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luzglongoria
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Thanks for your reply.
It is not a problem of memory since I can run other mapping analyses with no problem (I get big Sam output files w…
Comment: Translating gene names to entrez id's
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https://www.biostars.org/u/123097/ : Please post this as a new question. It is not directly related to this thread. Once you do that you ca…
Comment: Translating gene names to entrez id's
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Dear all,
I want to use the GoSim package to calculate the IC similarity. I'm trying to set the parameters of setEvidenceLevel(), but wr…
Comment: STAR is running but .sam file size does not increase after hours mapping
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Is this a server administered by a sys admin? Do you know if individual user accounts have "quota"?
If your user account has a storage qu…
Comment: STAR is running but .sam file size does not increase after hours mapping
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If I do
df -h
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Filesystem Size Used Avail Use% Mounted on
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It you really do have a reason to suspect that the biology of samples from CC1 is different from the biology of samples from CC2, and that …
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You don't show which species this is. I've taken a quick look at the human and mouse genome at those locations and neither have any genes a…
Comment: Annotating ENS codes to gene name
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This is a FAQ, Some past threads linked here: https://www.biostars.org/p/9552097/#9552101
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You are not running out of storage quota on the particular disk?
Comment: STAR is running but .sam file size does not increase after hours mapping
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I have tried reducing the number of threads but it is the same.
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1. Impossible to tell from the information you are showing. Could be misalignments, [read-through transcription][1] ([detection pipeline][…
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You can either use biomart to download all gene ids and gene names and then intersect them with your current table. Or you can use your ann…
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This does not work. I called for the gene "Cd8a" for instance for the mouse genome and it says "Gene not found" even though it should appea…
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Unfortunately it seems that *gaia* has been deprecated. You could still try to install a previous version of it, or set up a new conda envi…
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