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Comment: Help doing differential expression analysis -experimental design and gProfiler T
by
rajabolacuan
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Good Information Sir
Answer: Viral genes not showing up in combined mouse+virus alignment
by
cook.675
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200
Hello I was curious to follow up and wonder if anyone knew why the viral genes are not showing up in the count matrix? I can't seem to solv…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
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That makes sense. Thanks for the reminder.
Comment: bwa mem hangs after a few thousand reads
by
GenoMax
136k
Then you probably are best served by talking with your local sys admins to see where the issue may be.
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
> even if tpe and tbo are trailing after adapter and quality trimming
Priority/order of operations in coded in the program. Brian will be …
Comment: bwa mem hangs after a few thousand reads
by
cee28
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Actually, I originally did both of those things that you suggested. My original command at the top of the post was submitted to our cluster…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴
10
The number of bases is still different even if `tpe` and `tbo` are trailing after adapter and quality trimming. So far for the RNA-seq proj…
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
GenoMax
136k
No there should not be much impact unless one of the reads has become substantially short compared to its mate. Strictly speaking you don't…
Comment: bwa mem hangs after a few thousand reads
by
GenoMax
136k
> I am running this on a HPC cluster.
This is a guess but if you are actually running this on a cluster then it is possible that you need …
Comment: Discrepancy in total number of bases in trimmed read1 and read2 files after BBDu
by
CTLong
▴
10
Thanks GenoMax for the reply. That being said, does this difference in total bases between read1 and read2 have an effect in subsequent rea…
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters
by
DINESHR
•
0
Here are my PCA results plotted through Diffbind and Correlation heat map by deeptools shows some clustering in the samples @atpoint
version 2.3.6
version 2.3.6