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Questions tagged [linux]

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2
votes
0answers
34 views

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

I'm trying to run Repeatmasker in Linux on the command line with: ...
1
vote
2answers
163 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
205 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
225 views

Error in installing Vep

I am trying to installing Vep on Linux but an error is permanent ...
3
votes
4answers
224 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
272 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
votes
3answers
455 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
votes
1answer
135 views

How do I filter a GFF file by gene type?

I have a file with following information: ...
-1
votes
2answers
332 views

Script to run everything in a loop for extracting tar.gz files into fastq and to bam with alignment?

Original tar.gz files look like below: ...
1
vote
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 ...
0
votes
1answer
121 views

Why is my STAR reference genome indexing aborting on my GNU/Linux server but not on my Mac OS X laptop?

I am running the following command to index my genome: ...
-1
votes
1answer
152 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
votes
0answers
144 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
785 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.
3
votes
1answer
303 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-...
9
votes
5answers
469 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 ...
6
votes
2answers
261 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? ...