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Recent Replies
Comment: I have performed Trimmomatic run for adapter removal. QC report shows drop in th
by
swbarnes2
13k
The library is non-existent? The reagents got fried? The instrument failed? All of those will affect the assembly processes in a profoun…
Answer: How to find the most representative protein data base ID for your protein?
by
GenoMax
134k
Option 1:
Use MANE select proteins that you can download here (latest release as of today will keep changing) : https://ftp.ncbi.nlm.nih.g…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
Never tried, so idk. Why wouldn't it support it?
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
ATpoint
76k
I never tried conda images but since `mamba > conda` I guess mambaforge is better.
Comment: Filter human transcription factors
by
Chris
▴
180
Yes, I do GO and GSEA to get pathway. I download the background gene at https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp#C3 Th…
Answer: Visualize where kmers are on a reference genome
by
Alex Reynolds
35k
Make a bigBed file: https://www.biostars.org/p/9546293/
Then view it on the UCSC Genome Browser: http://genome.ucsc.edu/goldenPath/help/…
Comment: Integrated Seurat object change name of the two conditions
by
camillab.
▴
130
great! thank you very much!
Answer: Filter transcription factors
by
jared.andrews07
★
15k
[This database](http://humantfs.ccbr.utoronto.ca/download.php) has been the best I've found.
Comment: Filter transcription factors
by
Ram
40k
What have you tried? Have you looked at GO annotations?
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴
10
yes @juke34 , I tried agat_sp_compare_two_annotations.pl for both gff files and got comparative output in table format.
Thank you very muc…
Comment: Integrated Seurat object change name of the two conditions
by
Amitm
★
2.2k
Yes, its similar structure. This snippet should add a new metadata column "sample.New" with what you want to do
# Assuming a seurat obj. c…
Comment: Low Alignment rate
by
biofalconch
▴
970
Yeap, you can sample your reads with `seqtk` like this:
seqtk sample -s100 read2.fq 100 > Sample.fq
Take a couple and run them throug…
Answer: obtaining circular RNAs' sequences from circBase
by
Barry Digby
★
1.2k
You won't find them on circBase.
circAtlas has the mature spliced sequence available. You can [search for circRNAs](https://ngdc.cncb.a…
Comment: Should I Learn Docker to Run Command Line Bioinformatics Tool?
by
Ram
40k
\#TIL mambaforge - better than continuum's conda images I'm guessing?
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