Bioinformatics Questions, Problems & Solutions : TransWikia.com ~ Page 14

Separating peaks of chip-seq with specific length

My data contain several chip-seq results. I have the peaks called by MACS2.I wanted to only look at those peaks that their size is e.g 500bp to 1000bp. How can...

Asked on 08/19/2021

2 answer

Python script to simultaneously generate multiple pdbqt files for AutoDockTools?

I have a folder of pdb ligand structures that I'd like to test in some docking experiments with a certain protein using AutoDock Vina.I am not familiar with Python...

Asked on 08/18/2021 by sasam

0 answer

Read alignment using Bowtie2

So this is related to CRISPR-CAS9. I am working with off-target predictions for my thesis and was looking at all scientific papers related to CRISPR. I found one and decided...

Asked on 08/17/2021

1 answer

Treat methylation as binary or continuous signal when detecting DMR?

Methylation level is usually measured as continuous value (M-value from 450K). However, DNA methylation is binary outcome in nature (methylated or not), and it is relatively easy to make the...

Asked on 08/17/2021 by unicorn

0 answer

Loop Pymol command get_area

I want to select multiple residues from different PDB files loaded on the same pymol session.select resi LIGget_area seleHow do I loop the above command to enable the command...

Asked on 08/16/2021 by shome

1 answer

Apply trained PRS on another dataset

I am using PRSice to compute the PRS over a train set and want to use the coefficient used on the train set to apply it on another set which...

Asked on 08/15/2021

1 answer

How to map short sequences to long reads, recovering all multiply-mapped high-quality matches

The dilemma:I have around one million short sequences (21 bp to several 100s of basepairs) for which I need to identify all occurrences of in 20-30x coverage noisy long reads...

Asked on 08/15/2021

1 answer

Programmatically adding hydrogen and remove water to multiple PDB files

I'm trying to dock a ligand to several hundred PDB files (receptors).I thus need to prepare the those PDB files like removing water and adding hydrogen. I can do...

Asked on 08/13/2021

1 answer

How to use SRA Toolkit to blast SRA accessions?

I'm trying to look for a gene in a group of SRA files. Web BLAST can't cope with them, so I assume they're too large. I've tried tblastn_vdb from the...

Asked on 08/11/2021

0 answer

What is the meaning of split read?

I want to use rna seq data to later perform functional tests on fusion genes.so before that I need to filter the "best results" (of rnaseq) for deciding which...

Asked on 08/10/2021 by beachwildernessgene

1 answer

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