Questions tagged [bash]

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21 views

Download raw WGS files from MG-RAST on server

I want to download multiple fastq files from the MG-RAST database. However, these must be raw sequences. I am using the following on the server: ...
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19 views

running MAFFT on windows git bash

I'm pretty new to bioinformatics, I got some shell scripts from a senior who used to do things that I need to do, but these scripts were written on a Mac and I'm trying to set it up for Windows, ...
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1answer
20 views

Fastq-dump script download X spots or all

Im trying to write a script where an optional input of -X flag can be used, or if that info is not available download all reads. my script as follow: ...
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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 ...
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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 ...
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1answer
63 views

How I move these files based on their names in R or terminal

EDITED I have list of my samples in first column and corresponding file name for my .vcf files in second column of a file name clin_name.txt like below. For ...
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2answers
169 views

How to loop multiple function in shell script?

I need to extract sequences one after another consecutively from a large fasta files (multiple fasta files) and each extracted files to be saved in new fasta file (I mean the first sequence extracted ...
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2answers
32 views

Error with BWA Mem input having multiple fastq files using cat and process substitution

Running BWA Mem on a number of paired end fastq files using process substitution on the inputs results in this error: ...
2
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1answer
48 views

Pattern mining from a genomic sequence

I need to find the following pattern from a genomic sequence ...
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1answer
78 views

How to edit the headers of multiple fasta files from multiple folders? (recursively)

This is an expansion of my previous question, How to edit the headers of multiple fasta files from multiple folders? My directories are organized as follows: one main directory, in which I have ...
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1answer
41 views

How to edit the headers of multiple fasta files from multiple folders?

My directories are organized as follows: one main directory, in which I have multiple directories that end with a number ranging from 314 to 727, followed by .3 . For example, 'mgm4761314.3'. Within ...
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2answers
41 views

MiXCR: only create a single export file for all clonotypes

I am using following command from MiXCR to both align, assemble and export my input files: ...
2
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2answers
109 views

Filter reads belonging to unique sequences with threshold

I have CLL samples as fastq files and I want to remove those reads which have a unique sequence with less than 10 read counts each. I tried this by following way using awk to make it faster: ...
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1answer
28 views

How to run 'join' command for multiple files (of 2 types) in a folder

I have two types of files for a gene in a folder File 1: FOS.tf.txt ABL2 ACTN4 ADGRE5 ADIPOR2 ADRB2 ERCC4 EZR FAS FMO4 File 2: FOS.tt.txt ...
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1answer
75 views

How to combine multiple files into one file?

I have multiple files (n=86000) with one column each and I want to combine them all into one file with 86000 columns. I tried the following command ...
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2answers
80 views

how to remove range from fasta header

Could you please suggest me how I can remove range from fasta header:like these number from below sequences which has some colons indicating the range of the genome :147010-147657 :149201-149845 <...
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1answer
116 views

How to extract all pair end fastq.gz files from multiple subdirectory to a single folder

I have all file names for each paired-end fastq pair as shown below. Could you please suggest how I can extract all fastq.gz files in a single folder? sample name: ...
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2answers
71 views

How to extract values from second file on the basis common first column?

File1: ENST00000000233 ARF5 ENST00000000412 M6PR ENST00000001008 FKBP4 ENST00000001146 CYP26B1 ENST00000002501 DBNDD1 ENST00000002596 HS3ST1 File 2: ...
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22 views

Retrieve sequence data from just one geneID and not the identical sequences with blastdbcmd

I'm trying to retrieve the sequence from the gene id in NCBI's nr. If I try doing blastdbcmd -db nr -entry 1008808716 I get with this result: ...
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1answer
33 views

How to use extractfeat?

I am working on a script on bash linux to get the CDS (coding sequence) of a gene using extractfeat by EMBOSS. It gives me the error: Warning: No sequences written to output file I am unsure if my ...
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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 ...
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2answers
227 views

How to merge .fastq.qz files into a single .fastq.gz with their same id without losing any content in parallel

I have a large number of .fastq.gz files of different lane and reads. I have to merge them each reads group files into single .fastq.gz files. **eg: 1st type NA24694_GCCAAT_L001_R1_001.fastq.gz ...
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1answer
51 views

Multi-line efetch digging

I'm using efetch to dig out a middle "envelope" protein within a viral genome specifically within fasta format. The code below works but may not be robust for an entire database. Thus I want to ...
3
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1answer
592 views

What is a quick way to find the reverse complement in bash

I have a DNA sequence of which I would like to quickly find the reverse complement. Is there a quick way of doing this on the bash command line using only GNU tools?
3
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1answer
335 views

Running htseq-count over BAM files

I am trying to derive an expression matrix from BAM files using htseq-count on the server. These are bulk RNASeq BAM's by the way. I have read the ...
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1answer
23 views

How to use analysis output in my pipeline

I am running an analysis and I want to edit the output that I received from that analysis. However I cannot define the output name in my pipeline, because after running the analysis it is asking me to ...
3
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1answer
353 views

BAM to gene expression matrix (UMI counts per gene per cell),10X

I am trying to reproduce some results of a scRNASeq experiment. However I am new to the server-side aspect of such analyses and am very confused at the moment. The data provided by the authors of the ...
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2answers
65 views

Using preprocessing/alignment functions on the server

I am new to bash and the processes behind cluster computing in general and need some help with understanding some basics. After looking all over the internet and this forum (+ askUbuntu) I found ...
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2answers
440 views

Sort vcf by contig and position within contig

Due to tabix constraints, I need to sort a vcf so that contigs and then positions within contigs occur in numerical order in the vcf. I don't know if the following will sort positions within contigs, ...
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3answers
143 views

Replace lowercase characters with -

I have an output from vcfutils.pl vcf2fq with specified minimal depth, and it means that nucleotides with not enough depth are lowercase. I would like to change them to gaps. I could do it in higher ...
4
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2answers
114 views

How to align output of grep --color=always? (To QC fasta/fastq files)

Grepping out short sequences from a fasta or fastq file is a really useful way to look at sequencing data. Using the option --color=always makes this even more ...
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3answers
1k views

Bash scripting FastQC for multiple fastq files in multiple directories

I am completely new to bioinformatics so I'm looking to learn how to do this. I have multiple directories with fastq files: E.g; 10 Directories with each time series, each with Treatment and control ...
3
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0answers
142 views

Error given while trying to index a BAM file with Samtools Index - NO COOR?

I am currently working on my own Metagenomic pipeline, utilizing Bowtie 2 to map. Bowtie 2 outputs a SAM file, which I convert to a .BAM and sort it using Samtools. When I try to utilize Samtools to ...
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1answer
215 views

Extract certain fields using from GenBank file using Bash script

I need to extract certain lines from a GenBank file on Linux. Input file: ...
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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. ...