Questions tagged [command-line]
The command-line tag has no usage guidance.
15
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How to run a GATK Docker Image with local files?
I'm trying to use the HaplotypeCaller from the GATK toolkit but I keep getting an error. I pulled GATK through Docker and am using this command:
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1
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2
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54
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How can I limit blast results to exclude a specific taxonomic ID?
I would like to perform blast+, using the command line, here is the code:
-task blastn -db nr -outfmt 7 -query myQuery.fas -out result.txt -remote.
I have to ...
2
votes
1
answer
83
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Analysis of RNA sequencing with zUMIs
I wrote the .yaml file which was according the instruction from zUMIs:
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3
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2
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45
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what does 8 stands for in bwa mem command line
What does this command implies in bwa mem
bwa mem -t 8 index/referencegenome.fna read1.fastq.gz read2.fastq.gz > output.sam"""
What does ...
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2
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bcftool merge of 5K samples makes ID a large string
I am using bcftools to merge 5000+ vcf files using this command
bcftools merge -l list_of_vcfs.txt
I am getting the following error
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- 21
4
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2
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313
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Keeping DNA sequence after changing FASTA header on command line
I have a FASTA header that looks like this:
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0
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1
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49
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How can I change all text in a .tsv file to 1, except the first three fields?
I want to convert a .tsv file table in binary format (1 and 0). In which all cells containing text would become 1 and blank cells would become ...
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3
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2
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88
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Residue numbering in biopython
Is there an out-of-the-box function in the Bio.SeqIO module (in biopython) that can print a protein sequence (in command line) ...
1
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2
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79
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Combine separate fasta files from a list.txt
I have about 10 fasta files that I need to pull from a giant folder of other fasta files (has about 100 files). I have a list of the files I need in a .txt file separated by line and I want to pull ...
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97
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How can I identify the virulence factors in my FASTQ files generated from nanopore sequencing bacteria DNA?
I have performed genomic sequencing using nanopore technology and upon analysing using BLAST in the command line I have identified the presence of E.coli. I was wondering if I can add some code to ...
4
votes
4
answers
870
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How to get a file with the number of reads for several fastq.gz files?
I have generated several FASTQ files and I would like to know the amount of reads for each of them.
I am planning to run FastQC on the files which I know would give me the number of reads per sample ...
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4
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184
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How to remove empty files from a directory?
I have a directory of FASTA files, some of which are empty (placeholders that were output from a pipeline) and I would like to delete the empty files using a for loop on the command line.
From what I ...
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5
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472
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How to rename a file based on a directory name?
I have a lot of FASTA files that I recently scaffolded with RagTag. The output of RagTag includes a directory for each sample and the corresponding FASTA file written as "ragtag.scaffold.fasta&...
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3
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1
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317
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Using SED command in Nextflow script
I was wondering if someone can help me figure out this error message. I’m at the end of my Nextflow pipeline and I want to change the header in a FASTA file and it works when I use this command:
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2
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1
answer
87
views
Filtering file with AWK and writing output to new file
Hi I'm trying to filter a column in a PAF file with the AWK command and write it to a new file:
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