User: t_stranger

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t_stranger40
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Posts by t_stranger

<prev • 8 results • page 1 of 1 • next >
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Answer: A: AutoDockTools start software bug
... .pdbqt is a protein file format that support in the AutoDock software. The main purpose of using AutoDock is to doing Docking Analysis instead of convert pdb file to pdbqt file. If you only want to do the file conversion, openBabel is one of the options. Last time I used Windows GUI to run. I am n ...
written 3.4 years ago by t_stranger40
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Assessing coverage in exome capture experiments
... Hi, I am currently looking for how to draw the graph of depth of targeted region coverage, and I am trying to use bedtools and R to plot the graph. I follow the tutorial [here][1] but I am not understand how to interpret the graph and what is the meaning of Fraction of capture target bases >= dep ...
sequencing coverage targeted sequencing depth written 3.4 years ago by t_stranger40
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Comment: C: PDB visualization methods
... select the Zn ion ( ctrl + click the Zn ), invert the selection, hide the selection under action tab. Or u can select the residue under select tab. It can either run in command or graphic. If u prefer command, you can try to use it. Open the command line under Favourite tab ...
written 3.5 years ago by t_stranger40
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Answer: A: PDB visualization methods
... 1. UCSF Chimera 2. DS Visualizer Both softwares are free and able to visualize the pdb file format ...
written 3.5 years ago by t_stranger40
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Answer: A: Filtering FASTA sequences
... maybe can try to substitute the ID that start with symbol ">" to Hepatitis. You can do this in linux command sed 's/^ >.*/Hepatitis/' < hepatitis.fasta > NewIDHepatitis.fasta ...
written 3.5 years ago by t_stranger40 • updated 2.5 years ago by _r_am32k
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Answer: A: understanding bedtools coverage output
... column 9: RGB is the color that will show in the genome browser, every single color have its own code. Let's say (255, 0, 0) , it will show red color. column 13: Coverage Depth is how many reads in that particular nucleotide sequences. column 15 and 16 I seldom use, wait others to answer. ...
written 3.5 years ago by t_stranger40
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Comment: C: Amplicon Sequencing Data Analysis
... Thanks for your suggestion. May I know why we should not mark the duplicates before variant call? Because I read some resource they included it in the pipeline. ...
written 3.5 years ago by t_stranger40
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Amplicon Sequencing Data Analysis
... I am looking for a tutorial and journal of amplicon sequencing data analysis. Is there any specific free website to teach beginner the pipeline of data analysis and what should we report in our result. Any journal recommended? ...
amplicon sequence data analysis sequencing written 3.5 years ago by t_stranger40 • updated 3.5 years ago by WouterDeCoster45k

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