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Popular Question to
Omics data mining
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Carambakaracho
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3.2k
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kirillkirilenko
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bioinfo
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Recent Replies
Comment: How is "integer score for display" calculated in MACS2
by
SplitInf
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10
since this is one of the top search results, I'm cross-posting this comment from another user (alexbarrera)
"that the values of the 5th co…
Comment: Very low successfully assigned alignments with feature counts
by
Istvan Albert
99k
Load up your data in IGV and visualize it relative to your annotation file. It will tell you where the data aligns.
5% match on a 99% ali…
Answer: Ambient RNA removal method that generates whole (integer) counts
by
jared.andrews07
★
16k
I've definitely just rounded soupX output and had no issues with pseudobulking.
A colleague speaks highly of Cellbender, though it take…
Comment: Curated model organism gene functional annotations
by
manaswwm
▴
490
I thought Interproscan already has species-specific information, for example [this][1] page for Buchnera aphidicola. You can try to search …
Comment: Aligning sequences with multiple genetic codes!
by
5heikki
11k
I don't understand your problem. What do you mean when you write:
> These genes even in the same species may use different genetic codes.
…
Comment: An issue with gtf file (ballgownrsem)
by
cucindarko51
•
0
I also encountered issues when running ballgownrsem with gff files. Ballgown object was created, there is no informations about TPM and FPK…
Answer: Scanpy Pearson residual PCA error
by
Maëlick
•
0
I had the same problems and then realize that I forgot the preprocessing!
If you add this commands before running the PCA, it should work:…
Comment: Calculate GC content for entire chromosome
by
colindaven
5.8k
Try tripling your example seq length, see 20bp min region
-l INT min region length to output [20]
To answer your question, it …
Comment: Very low successfully assigned alignments with feature counts
by
GenoMax
136k
Is the genome/annotation from the same source i.e. Ensembl or so it appears?
Comment: Calculate GC content for entire chromosome
by
ATpoint
78k
What does this do? It's not documented well and does not work for me in terms of, it produces no output:
cat foo.fa
>chr1
GCGC…
Comment: Need help to find FASTA sequence from dbSNP
by
GenoMax
136k
Did you not see the last part in my comment above about how to get the sequence?
Comment: Need help to find FASTA sequence from dbSNP
by
syedahumairagillani
•
0
Thank you for your response.
Actually I am looking for fasta sequence of SNP as I shared via image, rather than just location. Would you p…
Answer: Calculate GC content for entire chromosome
by
colindaven
5.8k
The main one I use is stats.sh from the bbmap package (conda installable).
GC is 0.428 = 43% in this example. It's very quick.
stats.sh M…
Comment: Building reference dbSNP file using WGS samples
by
analyst
▴
10
I have employed your above suggested approach for BQSR (latter one).
I will try former approach too (that does not require reference vcf fi…
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