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Bioinformatics : Recent Questions and Answers (Page 30)

Find answers to your questions about Bioinformatics or help others by answering their Bioinformatics questions.

panic: division of zero by zero or infinity by infinity error when running GODON positive selection analysis

I am using godon to find genes under positive selection with the branch-site test. However, after running for a little while I get the error "panic: division of zero by...

Asked on 04/02/2021 by Samuel Zimmerman

1 answer

no result from heat map WGCNA

I have created a heat map using WGCNA using R. But the heat map command is not showing the plot and there is no error. I have a large number...

Asked on 04/02/2021

2 answer

Getting System.IO.FileNotFoundException with MaxQuant running on Linux with mono

I am getting this error with MaxQuant 1.6.14 running with mono (5.14.0.177=he1b5a44_1001).System.IO.FileNotFoundException: Could not find file "/home/ubuntu/run-dir/combined/combinedRunInfo"And I not sure why I am getting this error. The process has read...

Asked on 04/01/2021

1 answer

What unit is the length of a protein measured in?

Sorry if this question is obvious - I'm not familiar with proteomics so I'm not sure of the standard units. In this paper, it talks about using...

Asked on 03/31/2021

1 answer

How to sort multiple FASTA files based on their content?

I have around 10,000 FASTA files of Influenza A virus. These files contains sequences of each of the 8 segments of the viral genome and I want to separate these...

Asked on 03/31/2021

2 answer

How do I keep a glob from copying a file in Cromwell / WDL

Using Crowell 52. When I do a glob to get matching files, Cromwell places a copy of each matching file in the glob-* directory. As these are multi-gigabyte Bam...

Asked on 03/30/2021

0 answer

STAR aligner multiple fastq files

I’m using STAR to align fastq files from SMART-seq2. I have raw data folder containing sub-folders with samples names the sub-folders each contain fastq file. How can I make a...

Asked on 03/30/2021 by mobasher barsi

0 answer

What is the full script to extract sequences from fasta file by using Ids in text file in python 3 and pycharm?

I have a fasta file (gene.fasta)with sequences with names patterns: >Hsc_gene_9627.t1ATGGCACGCATTTTCCTCATTCTTTTATTGCTGCACAACATCTGCTGTGCAGCCGCTTCATTGCTCATTTTGAATGCCGTTACATTGGAGAAGGATGCTAATGATTATGCCGTTGGCGATand I have the Ids in text file (seq.txt) which are not the exact as in the fasta...

Asked on 03/27/2021 by Samer Habash

1 answer

extract chimeric and multimap reads from bam file

I am trying to extract all chimeric and multi-map reads from either SAM/BAM file. Is there any simple command to do that? Can I use htslib for parsing sam/bam files...

Asked on 03/26/2021 by SBDK8219

1 answer

Finding discriminating positions for a sequence alignment column

I don't have any theoretical background in biology, so forgive me if my question is a bit.. well..dumb. I'm trying to use a Monte Carlo approach to find the discriminating...

Asked on 03/25/2021 by space_gladiator

1 answer

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