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Recent Replies
Comment: Clustering and dynamic tree cutting
by
andres.firrincieli
3.1k
> it produces 160 clusters.
This is happening because the input is a simple correlation matrix that is affected by spurious or missing co…
Answer: When you convert a BAM back into a FastQ do you get the original Fastq?
by
GenoMax
125k
If the aligner writes reads that do not align by default to output (or you as the user chooses the right option for aligner to do so) then …
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…
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