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How should I interpret DGE results if only one HLA-A gene shows up as significant but not the others?

I have done a DGE recently and have been looking at the DGE list. One of the genes is HLA-A. However, when I dug deeper I realised there are hundreds of HLA-A genes with unique ENSEMBL number (of course it's HLA...). A few other HLA-A genes also…
Kento
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Genome-guided transcriptome reconstruction: should I filter my reference annotation by transcript_support_level or other tags?

Is there really any advantage to filtering the GTF annotation for transcriptome reconstruction (or, for example, for pseudo-alignment quantification)? Are there any downsides (i.e. reasons why I should NOT do that)? I'm going to run a transcriptome…
bepoli
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Can multiplexing in Sequel II SMRTcells reduce the coverage?

I would like to have high depth of coverage of the transcriptome, but I need to analyze several tissues. I was suggested to pool all 5 tissue samples in same SMRT 8M cell. Will this result in a smaller coverage when compared to non-multiplex…
Caterina
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How are BLAST record scores calculated in biopython

Can someone explain how the score is calculated for Bio.Blast.Record.Description? For example, if Record.Description.num_alignments is >1, is Record.Description.score simply the sum of the alignment scores for the description's hit? Can alignments…
Tim Kirkwood
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3
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2 answers

How can I find the maximum percent identity between two sets of (unaligned) sequences?

As the title states, I've got two sets of unaligned amino acid sequences (~25k sequences in one, ~3k in the other). I want to find the minimum distance between a sequence in the first set and a sequence in the second, expressed in terms of percent…
Empiromancer
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3
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2 answers

bash script for interproscan REST

hey i have the problem with bash script. It should run interproscan REST Im green in bash scripting. I found this script on the web: #!/bin/bash i=1 waitevery=30 mkdir -p out for j in $(find `pwd` -type f -name "*.fa") do echo "Iteration: $i;…
MTG
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3
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2 answers

STAR vs Bowtie2

What is the fundamental difference between STAR and Bowtie(2). Specifically, what is the difference in their final output (regardless of run-time differences, speed, memory usage etc.). Both seem to work on the same kind of input *.fastq files…
Zebra Fish
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3
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1 answer

Find a genomic coordinates for a protein aminoacid position

Is there a function that can map genomic position (hg19) back from a protein position? I can have name of a particular transcript, and exon number. For example, I have KRAS gene for which I would like to know the exact genomic position of G12, and I…
lizaveta
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How To display bar graph with error bars?

I am using the below code to get the bar plot. I want to get the bar plot with error bars displayed. import seaborn as sns def plot_coefficients(target, coeffs_df, n=10): if coeffs_df.shape[0]==0: return None # nothing to plot here! …
Megha
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How to use hgvs to project a variant list on a given protein sequence string?

I have the following protein structural variance list: mutations = ['F594_D600dup', 'D586_E596dup', 'D593_F594insSPEDNEYFYVD', 'E598_F612dup', 'E598_Y599insSGSSDNEYFYVDFREYE', 'E598_Y599insVAYVDFREYE', 'E604_F605insSPRGGNEYFYVDFREYEYDLKWE',…
0x90
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3
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2 answers

R ggtree apply colors to branches with multiple colors

This question was also asked on StackOverflow I have a phylogenetic tree made with a Newick format ((a:1,b:1):2, (c:1, d:1):3):1; The output will be I have drawn this with http://etetoolkit.org/treeview/, but output with R will be same. What I…
SG Kwon
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3
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2 answers

Example of a small but moderately complex PDB file?

I am developing a bioinformatics framework only for learning purposes. I want to calculate -- dihedral angles detect H, E, and C components detect Hydrogen bonds etc. Therefore, I want a PDB file that represents a protein with a small chain but is…
user366312
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1 answer

How can I parse alternative atom information?

I am trying to parse PDB files. Say, a PDB file has the following data: ATOM 33 N ATHR A 2 4.935 -11.632 15.046 0.74 2.95 N ATOM 34 N BTHR A 2 5.078 -11.406 15.180 0.31 2.78 N ATOM 35 CA…
user366312
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What is the function of the heteroatoms

I am trying to make a prediction application using the sequence of proteins. If we think about the 6COU protein, I'm running the code below pdb = PDBParser().get_structure("6c0u", "6c0u.pdb") for residue in pdb.get_residues(): print(residue)…
drorhun
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3
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1 answer

deseq2 makeContrasts function

This article talked about various deseq2 designs etc. One of the designs I would like to use is explained as this: Control versus treatment average makeContrasts((treatmentI+treatmentII+treatmentIII)/3-treatmentCTL, levels=colnames(design)) I'm…
kcm
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