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Recent Replies
Comment: RNAseq requirements: Biological and Technical replicates
by
jkim
▴
220
Ouch, my mistake. Updated my comment.
Comment: RNAseq requirements: Biological and Technical replicates
by
i.sudbery
22k
However, one might argue that multiple biological samples (i.e. multiple blood draws) from each patient might be useful. Still, probably no…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
Mensur Dlakic
★
29k
> So maybe this approach will help us find interesting and rare pathways — something along those lines.
Still the same answer as before - …
Comment: ATAC-seq fragment size distribution - huge spike at 150 bp
by
yuntan1992
•
0
or add parameter "--soft-clipped-unmapped-tlen"
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions
by
ATpoint
89k
I would take this opportunity to encourage using different tools. Cibersortx is not open, its source code has never been published. That ha…
Answer: CIBERSORTx error: 'x' must be an array of at least two dimensions
by
catarinaventura_pt
•
0
For those still looking for the answer about this, I just figured out that you need to have replicates for it to work.
Comment: CIBERSORTx error: 'x' must be an array of at least two dimensions
by
catarinaventura_pt
•
0
I´m having the same problem here described. Any updates on how to solve this?
Answer: ATAC-seq fragment size distribution - huge spike at 150 bp
by
yuntan1992
•
0
After removing adapters with trim_galore, change the parameter of bowtie2 " --local" to "--end-to-end".
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
shevch2009
▴
20
That is a great comparison! :) It definitely looks that way. :)
It's not about taxonomy, but about reconstructing metabolic pathways direc…
Comment: How to connect the UCSC when i get the DMR.plot?
by
Wren
•
0
I tried using the main site but it still didn't work. Thanks anyway, I'll try other methods.
Answer: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
Mensur Dlakic
★
29k
If you want an overall taxonomic profile, this tool will do it from reads directly:
https://github.com/DessimozLab/read2tree
> Well, …
Answer: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
LChart
5.0k
I have used BURST (https://github.com/knights-lab/BURST) to do this before. You can take fastA sequences for your target genes and build ou…
Comment: RNAseq requirements: Biological and Technical replicates
by
Ram
45k
Why not just say "technical replicates are necessary"?
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
shevch2009
▴
20
Well, we already have mags, but my boss want to check the raw reads, that is why I am trying to find a way.
Well, human got me errors, it…
Comment: Tools for raw reads that estimate the percentage of reads that hit marker genes
by
GenoMax
153k
Then you need to decide if you want to assemble your reads into contigs/MAG's followed by using the tools discussed. Or do the mapping usin…
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