Questions tagged [linux]
The linux tag has no usage guidance.
18
questions
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:
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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.
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1
vote
1answer
225 views
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:
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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.
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2
votes
1answer
135 views
-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:
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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:
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-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?
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