Questions tagged [linux]

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votes
2answers
67 views

How can I run a command for multiple files?

Good evening, I have a bunch of .vcf files in a folder and I want to run command below on all of them but doing that one by one manually is really painful. I am ...
0
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2answers
54 views

How I can run this code on my files?

I am annotating some .txt files by Annovar software by this code ...
1
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0answers
37 views

TBLASTN error: Too many positional arguments

I was running tblastn using standalone blast2.9.0+ through Ubuntu Linux, to get the alignment result of a list of protein sequences for same species, against its complete genome file. The command I ...
0
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0answers
8 views

How to install senaite.lims on Ubuntu 18.04? [migrated]

I am trying this: https://www.senaite.com/docs/installation but I am running into tons of errors along the line. If anyone managed to install this program on Ubuntu 18.04, I would be happy to see some ...
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2answers
23 views

How to convert mzXML to mzML format (mass spectrometry files)?

How to convert mzXML to mzML format (mass spectrometry files) preferably under Linux and/or Python?
1
vote
4answers
93 views

How I can change the name of multiple files at once in R or terminal?

I have 200 .vcf files in a folder with long names like LP6005409-DNA_E03_vs_LP6005408-DNA_E03.snp.pass.vcf How can I change the name of each file to, for ...
3
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4answers
126 views

How to download FASTA sequences from NCBI using the terminal?

I have following accession numbers of the 10 chromosomes of Theobroma cacao genome. ...
0
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1answer
26 views

Replacing some strings in R or terminal

I have a .txt file; I have 139 unique sample IDs in sampleID column ...
2
votes
0answers
42 views

“perl: warning: Setting locale failed.” in RepeatMasker

I'm trying to run Repeatmasker in Linux on the command line with: ...
1
vote
2answers
204 views

processing fastq files using cellranger on linux

I am trying to perform a cellranger count on fastq files generated from a 10x genomics single cell RNA Seq run. Just to provide some background, I ssh’d into the AWS using our AWS IP with MobaXTerm ...
3
votes
2answers
264 views

Installing DESeq2 in Ubuntu

I am trying to install DESeq2 in my Ubuntu with R version 3.5.1. According to the package repository in Bioconductor the version should be 3.5. ...
1
vote
1answer
280 views

Error in installing Vep

I am trying to installing Vep on Linux but an error is permanent ...
3
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4answers
264 views

How to run same command on multiple files?

Hi im doing Variant calling on fastq files for which i have 4000 fq files and the variant calling are done in different 9 steps. Each step generate different files that are output to next steps. So ...
3
votes
1answer
306 views

Downloading multiple SRA files from several SRA accession IDs does not work

I am trying to download multiple SRA files located in several SRA accessions. Some of my accession numbers are as follows: ...
5
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3answers
488 views

finding unique headers in a fasta file using linux command line

I tried to use the following command uniq -u reference.fasta >> reference_uniq.fasta I'd like a count of the unique headers.
3
votes
3answers
79 views

How to get the product of a CDS

I need the name of the protein in /product="protein_name" using bash commands. Beware, there is a lot of whitespace between lines. ...
2
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1answer
158 views

How do I filter a GFF file by gene type?

I have a file with following information: ...
-1
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2answers
359 views
1
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1answer
39 views

Installing Rostlab's PredictProtein

I am trying to install Rostlab's PredictProtein in a Virtual Machine as detailed here https://rostlab.org/owiki/index.php/How_to_Run_The_PredictProtein_Machine_Image_with_VirtualBox: Download ...
9
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5answers
477 views

Using shells other than bash

As someone who's beginning to delve into bioinformatics, I'm noticing that like biology there are industry standards here, similar to Illumina in genomics and bowtie for alignment, many people use ...
0
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1answer
130 views
-1
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1answer
172 views

Unable to Install PGDSpider using Ubuntu and wine

I'm running wine v 2.0.3 using ubuntu v. 16.04.2 on a Mac. I'm trying to install a program called PGDSpider2 from here. Essentially the program is supposed to convert different file formats used for ...
3
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0answers
153 views

How to submit a canu job on LSF high-performance computing cluster farm?

I am currently running canu on an LSF Linux server using the following script called assemble.sh: ...
7
votes
7answers
809 views

What are the available cloud computing services for bioinformatics? [closed]

I'm looking for cloud computing services that can be used for doing bioinformatics. An example I found is InsideDNA and there is Amazon of course. A little description of these would be appreciated.
6
votes
2answers
278 views

Parallel processing of scripts that use obitools

I have an obitools script (de Barba et al. 2016) that I would like to run faster. How would you run it in parallel to cut down on time? ...
3
votes
1answer
312 views

How to extract exome on-target reads in batch?

I was given a list of target regions in BED and many exome alignments in BAM. I was asked to extract on-target alignments from these BAMs to save disk space. I know I can use bedtools to extract sub-...