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Recent Replies
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the
by
Spring
•
0
Thank you very much!
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the
by
Spring
•
0
Thank you so much! If the 10x Chromium protocol is not used, should the processing be done with HISAT2, FeatureCounts, and so on?
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the
by
fracarb8
★
1.6k
For the paper, they used the `indrop` pipeline (https://github.com/indrops/indrops), and you should have a look at it, and try to run with …
Comment: I'm new to cell ranger. Can single cells prepared with a protocol other than the
by
ATpoint
81k
CellRanger is specific for 10x Chromium. I did not check the details of this single-cell platform so I recommend to see what papers that us…
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
by
Pierre Lindenbaum
161k
<!-- The New York Times is an American daily newspaper based in New York City. The New York Times covers domestic, national, and internatio…
Comment: Tumour purity and ploidy estimation
by
Lloyd98
•
0
Hello bp22,
I'm in the same situation as you, I have Whole Exome Sequencing data for tumour samples only, with no normal samples. I haven'…
Comment: Ensembl gene id conversion
by
naveedhasan2000
•
0
I actually have a list of ensembl ids generated while doing a read count using htseq, i used the reference genome from ensembl. I then trie…
Comment: Odd results with BLAST remote
by
b.contreras.moreira
▴
150
See https://www.biostars.org/p/9486493 and parameter `-max_hsps 1`
Answer: WGCNA network from Adjacency or TOM matrix
by
andres.firrincieli
3.6k
Since the module detection is performed on the TOM, you should go for the TOM.
Answer: Error in edgeR/Deseq2 Analysis
by
kuttibiotech2009
▴
30
The error message you're encountering suggests that there might be duplicate row names in your input data file. check it once again whether…
Comment: Getting marker genes for cell types
by
orzrzlyo
▴
20
Thank you! Also, cell typist would successfully identify the above cell types, however, they seemed to be in a pretrained or pre-organized …
Answer: Getting marker genes for cell types
by
LChart
3.9k
It seems strange that celltypist would not identify these major cell classes -- you should double check your data quality. For the marker l…
Answer: gene body coverage with RSeqQC
by
jkim
▴
170
http://qualimap.conesalab.org/doc_html/index.html
Never tried rseqc, but qualimap provides a gene body coverage plot also.
Comment: How to get the reference panel sites for TOPMed hg37 and 38
by
bk11
★
2.3k
You can simply impute your genotyped data in TOPMed server. In that way you do not have to deal with downloading the reference panels (not …
Answer: Using adonis to include a random effect
by
LChart
3.9k
> why the first model doesn't have stats for both variables?
Your variables are multicollinear. This will always be true if you have mul…
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