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Istvan Albert
98k
Popular Question to
windsur
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dukecomeback
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poltora4enko
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biofalconch
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Recent Replies
Answer: Is it possible to convert 3 prime sequencing read counts into TPMs?
by
Trivas
★
1.4k
No, since 3' end sequencing is basically counting individual transcript abundances. You could probably get away with dividing the counts pe…
Answer: Mapping SNP rsIds/ positions to genes coding for proteins
by
Alex Reynolds
35k
Here's one way to do it:
To get SNPs, assuming you are working with `hg38` human GWAS data:
```
wget -qO- https://ftp.ncbi.nlm.nih.g…
Comment: how to identify uniq genes between two gff files.
by
nikhil
▴
20
yes @juke34 , both results are almost similar.
Comment: What is the correct procedure to generate a consensus bacterial sequence?
by
Istvan Albert
98k
What I would do after step 2 is look at and evaluate the resulting BAM alignment file with IGV.
Do you have variants? Are these variants i…
Comment: What is the correct procedure to generate a consensus bacterial sequence?
by
Mensur Dlakic
★
25k
Is there any reason not to attempt the assembly after step 1? The assembly is a "consensus" of all short reads and can be directly compared…
Comment: Mapping SNP rsIds/ positions to genes coding for proteins
by
Pierre Lindenbaum
157k
https://www.biostars.org/p/384185/#417225 ; https://www.biostars.org/p/413/
Comment: Troubles launch IGV on Linux(Debian)
by
PoscaXVIII
•
0
Here the output I got
MyPC@Debian:~$ lsb_release -c
No LSB modules are available.
Codename: bookworm
MyPC@Debian:~$ ls…
Comment: Bacterial Pangenome Analysis
by
kirankumareripogu
▴
10
Hi @liorglic,
Thank you so much for your response.
This provides a clarification to most of my doubts and questions regarding pangenome …
Comment: Troubles launch IGV on Linux(Debian)
by
PoscaXVIII
•
0
Hi,
Thank you for your help. I tried both of your suggestions. Regardless of the version installed (tried 4 different versions), the resul…
Answer: Number of accessible regions included by DESeq2 to generate the PCA plot with th
by
jespinosa
•
0
Hi,
The one rendered in the multiqc report corresponds to all genes and if you go to the corresponding path in your results folder you wil…
Answer: Where to find info on VCF file format?
by
Ram
40k
Adding on to Shred's answer, VCF is flexible and self-describing so you won't find the meaning of all fields in your VCF in the file specif…
Answer: Number of accessible regions included by DESeq2 to generate the PCA plot with th
by
Alexandre Eeckhoutte
•
0
Hello,
If you follow this logic then it would be the top 500 most variable accessible region no ? (my question is not clear maybe, but I…
Comment: Where to find info on VCF file format?
by
Ram
40k
You need to read manuals carefully before asking questions here. It's literally right there in the link in your post: https://samtools.gith…
Comment: How to filter vcf file by MAF using bcftools?
by
Ram
40k
IMO that cheat sheet is quite confusing. The official manual is a lot clearer. OP needs to read the freaking manual, especially if they can…
Comment: Does anyone know how to download genBlastG?
by
dukecomeback
▴
40
Glad to let you all know, there is a new tool provided by Heng Li: **miniprot**, you will like it.
By the way, is there any one thinking a…
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