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Recent Replies
Comment: STAR is running but .sam file size does not increase after hours mapping
by
GenoMax
125k
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
by
luzglongoria
▴
40
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
by
GenoMax
125k
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
by
eliska.ochodkova
•
0
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
by
GenoMax
125k
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
by
luzglongoria
▴
40
If I do
df -h
then I get
Filesystem Size Used Avail Use% Mounted on
devtmpfs …
Comment: RNASeq differential expression masked by pathways disregulation
by
i.sudbery
16k
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 …
Answer: High downstream gene expression
by
i.sudbery
16k
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
by
GenoMax
125k
This is a FAQ, Some past threads linked here: https://www.biostars.org/p/9552097/#9552101
Comment: STAR is running but .sam file size does not increase after hours mapping
by
GenoMax
125k
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
by
luzglongoria
▴
40
I have tried reducing the number of threads but it is the same.
Answer: High downstream gene expression
by
Matthias Zepper
2.9k
1. Impossible to tell from the information you are showing. Could be misalignments, [read-through transcription][1] ([detection pipeline][…
Answer: Annotating ENS codes to gene name
by
Apex92
▴
240
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…
Comment: CoveragePlot in Signac from MACS2 Object
by
bioinformatics.girl
•
0
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…
Comment: How to extract the list of genes from TCGA CNV data
by
Kevin Blighe
84k
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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