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Recent Replies
Comment: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
by
GenoMax
150k
> remove these tags and realign these sequences
While we don't know how many other labs/users are going to use this data, since there are…
Comment: convert Gene ID to Gene Symbol
by
GenoMax
150k
Using `EntrezDirect` ([**LINK**][1]) you can look these up at NCBI:
$ esearch -db gene -query "hsa-let-7a-3p" | esummary | xtract -pat…
Answer: Which tools use or rely on the XA tag in SAM/BAM/CRAM files?
by
Istvan Albert
102k
One workaround could be to remove these tags and realign these sequences if you ever needed the XA tags alone.
The mapping quality will …
Comment: Is Centering and Scaling Essential for Expression Data as Input for Machine Lear
by
Istvan Albert
102k
I'll put this in a comment since I am mostly guessing here. But I'd say that if the data was comes from a single experiment, all normalized…
Comment: Steps for meta-analysis
by
majorprogeria
•
0
this is an pipeline that i am following "https://nbviewer.org/github/metaOmics/tutorial/blob/master/metaOmics_turtorial.pdf" i could'nt use…
Comment: convert Gene ID to Gene Symbol
by
majorprogeria
•
0
this one of the example
"customerID
# uniSp.2
# uniSp.4
# uniSp.5
hsa-let-7a-3p
hsa-let-7a-5p
hsa-let-7b-3p" …
Comment: Query coverage high, E-value low, and identity low - Blastp results interpretati
by
Mensur Dlakic
★
29k
I didn't learn this by reading a single book or an article, so nothing like that comes to mind. Some random resources:
- https://www.biost…
Answer: Single Nuclei RNA-Sequencing Analysis Without CellRanger
by
dsull
★
7.3k
Hmm, what aligner are you using? STARsolo will automatically put the barcodes into the CB:Z: tag in the BAM file.
Otherwise, I believe y…
Comment: GTF repeatmasker annotation file
by
rfran010
★
1.4k
I would also recommend the Hammell Lab's curated GTF files:
https://www.dropbox.com/scl/fo/jdpgn6fl8ngd3th3zebap/ACdZkShDC1au-OckIipI5kM/T…
Comment: GTF repeatmasker annotation file
by
rfran010
★
1.4k
Are you referring to the third column "exon". That is a placeholder of sorts. You can check a couple loci manually to confirm they don't al…
Comment: Query coverage high, E-value low, and identity low - Blastp results interpretati
by
Luana JBC
•
0
Could you recommend an article or a book?
Comment: Methods for directional pathway analysis of DEGs?
by
Gordon Smyth
★
7.9k
Yes, I had already noted in my answer that the GO and KEGG annotations are not directional, meaning that genes in a GO term or KEGG pathway…
Comment: Query coverage high, E-value low, and identity low - Blastp results interpretati
by
Luana JBC
•
0
Hi, Mensur! Thank you very much for your explanation.
Best regards!
Answer: Unable to generate hierarchical and circle plot using CellChat
by
S
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I spent days on this and funnily enough the minute I post about it, I solve the issue!!
There were 2 problems:
1. vertex.size = groupS…
Comment: Steps for meta-analysis
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ATpoint
87k
Can you please elaborate what you aim to reveal with your "meta-analysis". Frankly, that you mention meta-analysis and fastqc in the same s…
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