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natasha.sernova
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Genotepes
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vkkodali_ncbi
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i.sudbery
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Recent Replies
Answer: Using Entrez Utilities to query the Nucleotide database by collection_date
by
GenoMax
125k
Using [**Entrezdirect**][1]. Date in last column is collection date. No way to query using it though. Could be wrong.
$ esearch -db nu…
Comment: Faking hh-suite workflow / alignment output
by
Mensur Dlakic
★
22k
Pretty sure that nothing other than HHsuite outputs results in `.hhr` format.
Answer: Manual Polygenic Risk Score calculation
by
Sam
★
4.6k
Same allele = weight of 1, different allele = weight of 0. You can read more here: https://choishingwan.github.io/PRS-Tutorial/plink/#gener…
Comment: Single sample GSEA analysis
by
tujuchuanli
▴
100
Hi jv,
Thank you for your help. But I am still uncertain. The GSEA tools can process the preranked list. However, it still required that I…
Answer: 2D structure of a custom protein (not in any databases) from a PDB file.
by
Jiyao Wang
▴
290
You can also try out [iCn3D](https://structure.ncbi.nlm.nih.gov/icn3d). After you load your custom PDB via the menu "File > Open File > PDB…
Comment: CoveragePlot in Signac from MACS2 Object
by
bioinformatics.girl
•
0
What is 'peaks' entered as?...
The input is:
CoveragePlot(
object = pbmc,
region = "CD8A",
ranges = peaks,
…
Comment: Faking hh-suite workflow / alignment output
by
Nick
▴
40
I totally get your point, maybe long-winded was also not the right description for my issue. One example, [custom databases][1] are very cl…
Comment: CoveragePlot in Signac from MACS2 Object
by
seidel
10k
Wouldn't you take your MACS2 files, import them with rtracklayer so that they are GRanges objects, and then pass those as the peaks? i.e. w…
Comment: RNAseq for DE purpose
by
swbarnes2
13k
Honestly, I think most RNASeq aligners are fairly robust to adapters. You could probably get away with not trimming at all
Comment: Analyzing bulk RNA-seq
by
swbarnes2
13k
To paraphrase another poster here, you are asking how to get a cow out of a steak. You can't do it. A bulk RNASeq experiment does not cont…
Comment: RNAseq for DE purpose
by
GenoMax
125k
Use following:
for i in `ls -1 *R1*.fastq.gz | sed 's/\_R1.fastq.gz//'` do echo trimmomatic PE -phred33 $i\_R1.fastq.gz $i\_R2.fastq.g…
Comment: Alien-hunter outputs
by
GenoMax
125k
This answer does not help future visitors. If you found the explanation then edit the answer and please post it here.
Answer: Faking hh-suite workflow / alignment output
by
Mensur Dlakic
★
22k
> Everything in hhsuite feels very long-winded.
Complex programs with many options are either properly explained for the non-TLDR crowd, w…
Answer: RNASeq differential expression masked by pathways disregulation
by
ATpoint
68k
Tools like DESeq2, edgeR and limma recommend in their manuals to include covariates such as batch (here that is center) into the model. Try…
Comment: VCF to Plink files
by
hi.there
•
0
Thank you. I added --allow-extra-chr and a .fam file was made. Is that output correct?
./plink2 --vcf out.hg38KeepVariants.vcf --make-jus…
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