Questions tagged [shell]
The shell tag has no usage guidance.
48 questions
2
votes
1
answer
64
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windows shell -- running igblast: "BLAST query/options error: Germline annotation database ... internal_data directory cannot be found"
I'm trying to run igblast from NCBI in windows powershell. When following the documentation and trying to run the following code:
...
- 31
3
votes
1
answer
54
views
Passing data from the Agilent Trimmer utility to bwa-mem2 via a named pipe
I am trying to use a named pipe to pass data from the Trimmer utility from the AGeNT toolbox from Agilent, through bwa-mem2. The normal behavior is that the Trimmer utility writes trimmed fastq files ...
2
votes
2
answers
68
views
Python/R/bash script to ease the comparison of different protein complexes in PDB
I would like to create a table of comparison among similar protein complexes from the pdb.
This would be based on their numbers of proteins and the presence of each protein.
Is there any way like ...
- 31
1
vote
0
answers
47
views
Need to find an intersect of sequences inside fasta files (no standardized sequence names)
I have several multifasta files (each containing between 3,000 to 3,600 sequences). The sequence names were derived from the genome where the sequence was extracted and they bear no significance or ...
3
votes
1
answer
277
views
Multiple SRR ID downloaded for single GSM IDs input issue
So here I'm trying to donwload multiple fastq files based on the GSM ID input the script works fine when then input is only SRR id but it runs into error when it is given GSM ID
My small GSM ID input ...
- 207
3
votes
1
answer
484
views
ncbi fastq dump error in loop
I have a very basic objective which I want to give list of id to a ncbi-srafastq tool kit which will prefetch the id which is in .sra file extension and then it will run fastq-dump on the file to ...
- 207
3
votes
1
answer
114
views
Extract specific nucleotide base position for query and subject from text file
I have an input file looks like this:
...
- 31
1
vote
1
answer
116
views
Replace a string in a column of a text file based on matching string listed in another file using Linux
I have multiple sets of files, so I grepped the list from a column in a separate file such as file1.txt. I want to change all other files by using this ...
- 157
0
votes
0
answers
120
views
How to Split VCF File into male and Female groups
Cross-posted on biostars
I have trio_example.vcf file and I want to split them into male and female groups. I tried this:
$ bcftools query -l trio_example.vcf
And ...
- 35
-1
votes
1
answer
41
views
How can I transform this String?
Good afternoon, I'm a bioinformatics student and I'm trying to put some strings between commas with a space. The output looks like this: ...
- 21
-1
votes
1
answer
26
views
How can I tranform this String?
I'm trying to alter this string: NC_037078 1:122545 124035 into this: NC_037078.1:122545-124035 but I don´t know how.
The ...
- 21
2
votes
1
answer
500
views
How do I cut a genome into one specific region?
Good morning, I study bioinformatics and I need some help with a work. I have the NCBI accession numbers for the species I want for example: NC_037078.1 and I have the specific coordinates where I ...
- 21
2
votes
1
answer
132
views
Error Registering Job Definition AWS
I am in the process of creating a bioinformatics pipeline and I am currently trying to setup the AWS infrastructure for which it will run.
The script I am running to setup the AWS batch job looks like ...
- 101
2
votes
3
answers
293
views
How do I find unique file names without their extensions in shell script?
I need to generate a list of unique file names without their extensions or using the shell script command "find"
Say I have a list such as:
...
- 361
0
votes
2
answers
560
views
Remove from Multi-FASTA by Sequence ID
I want to remove sequence VRE32514 – it doesn’t belong and thus is the reason it lacks additional metadata. However I tried implementing this code from a similar question:
...
- 63
1
vote
2
answers
262
views
Pulling a numbered chromosome range file given a gene location from a lookup table ideally from command line or R
have a folder with roughly 1000 vcf files which have divided the human genome into chunks, the folder looks like this:
...
- 163
1
vote
1
answer
59
views
how to repeat records in fastq n times efficiently?
How to iterate/repeat a record n times in a fastq file using bioawk? I wrote a python code using biopython, but it is very very slow. So, I am wondering if I can get some help by using bioawk. Thank ...
- 13
2
votes
0
answers
75
views
Why do I obtain different output results with blast vs awk commands
I have an awk command that identifies 30 pb from two multifasta files.
When I used two input files:
E.g. 100 sequences each, I get the same result with the ...
- 41
1
vote
1
answer
83
views
Metagenome simulation from a concatenated FASTA file
I am trying to simulate metagenome sequencing. So I will start with a file with a lot of concatenated genomes. From there, I would like to randomly extract 10,000 sequences of length 200bps.
I got ...
- 41
1
vote
2
answers
1k
views
How to replace sequence identifiers in a fasta with OTU IDs from another file?
I'm pretty new to Unix and bioinformatics and having a hard time accomplishing the following. I have one FASTA file with sequences and headers, and one OTU ID mapping file (.txt) with OTU IDs and ...
- 11
2
votes
1
answer
184
views
awk shell script
I have a folder named quant. Inside this folder I have 27 folders named SRR8068516_quant to SRR8068543_quant. I want to edit a file inside these folders titled quant.sf and produce an output. I ...
- 143
2
votes
1
answer
1k
views
remove sequences from fasta file matching a string in the header
I have a file with 16S sequences. some headers contain species information. For my purposes I would like to exclude a number of species from the file, therefore I would like to do a pattern matching ...
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1
vote
1
answer
363
views
processing multiple fastq files with cutadapt
I have DNA sample from 5 pools, having 25 fastq files each. I am running cutadapt to remove the primers using this command
...
- 143
0
votes
1
answer
110
views
1
vote
1
answer
63
views
move files of a different group to separate directory
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 ...
- 2,232
1
vote
1
answer
72
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:
...
- 59
0
votes
2
answers
137
views
How I can run this code on my files?
I am annotating some .txt files by Annovar software by this code
nnovar]$ module load annovar/2016Feb01
[cyan01 annovar]$ table_annovar.pl
But I really got ...
user6517
1
vote
1
answer
556
views
Peak-calling using homer
I have a total of 78 ATAC seq samples from which Im trying to do a peak call .I tried this batchParallel.pl findPeaks peaks function but i couldn't find the output ...
- 1,854
0
votes
2
answers
658
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 ...
- 109
1
vote
4
answers
2k
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 ...
- 2,232
2
votes
1
answer
78
views
Pattern mining from a genomic sequence
I need to find the following pattern from a genomic sequence
...
- 109
1
vote
1
answer
2k
views
for loop cutadapt for files on a single directory
I have a bigfolder where i have a lot of fastq.gz files and I want to remove the adapters from all of them.
I am trying then the following loop:
...
- 23
2
votes
3
answers
1k
views
How to reverse complement the DNA sequences for given inverse/reverse coordinates?
I have the series of coordinates in id.txt file, whose coordinates sequences are in genome.fasta file.
The coordinates of id.txt ...
- 109
-1
votes
1
answer
118
views
3
votes
2
answers
24k
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
...
- 73
1
vote
1
answer
1k
views
removing mitochondrial read and unassembled "random" from multiple bam files
This is the one i used for a single bam file to filter its mitochondrial as well as unassembled read
...
- 1,854
2
votes
1
answer
542
views
Executing PyMOL from a Shell script
I'm trying to execute pymol from a shell script (and it is not working). I'm not executing the script on PyMOL but even if I do this, it doesn't work neither. However, if instead of a script the ...
user4378
1
vote
1
answer
508
views
Batch alignment of inconsistently named Fastq files
I have numerous gzip-compressed paired-end Fastq files with ChIP-seq data that I would like to align with bowtie2. I confirmed that bowtie2 takes .gz files, ...
- 1,854
1
vote
0
answers
92
views
"Bad substitution" error while trimming adapters [closed]
I have this script to trim adaptors from my fastq sequencing files
for PAIR in $(fastq | sed 's/_R.//g' | uniq)
I am gitting this error: bad substitution
Could ...
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5
votes
1
answer
3k
views
Splitting fasta file into smaller files based on header pattern
I have to split this fasta files into smaller files and write them into individual files my files
...
- 1,854
2
votes
0
answers
137
views
group samples based on shared mutations in a single multi samples vcf file
I am learning about vcf file formatting and have a multi-sample (>300) vcf file and aim to group (take) samples with shared mutations.
Can someone suggest a tool/command/script solve this problem?
- 199
5
votes
1
answer
264
views
Bash script error at paste command
I wrote script for pasting rsids on CADD output. Here is script.
...
- 105
2
votes
3
answers
174
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 ...
- 123
2
votes
1
answer
1k
views
9
votes
10
answers
25k
views
Remove/delete sequences by ID from multifasta
I have a fasta file like this:
>Id1
ATCCTT
>Id2
ATTTTCCC
>Id3
TTTCCCCAAAA
>Id4
CCCTTTAAA
I want to delete sequences that have the following IDs.
<...
- 385
8
votes
1
answer
723
views
Using a Bash Script to search TaxIDs against NCBI's Taxonomy yields "400 Bad Request" error?
I've been searching TaxIDs against NCBI's Taxonomy DB to get taxonomic lineages for species. I have successfully done this for 1,000's of TaxIDs that were returned to me by Blast+ blasts in a CSV. (...
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13
votes
4
answers
792
views
How do I efficiently subset a very large line-based file?
This has come up repeatedly recently: I have a very large text file (in the order of several GiB) and I need to perform line-based subsetting for around 10,000 lines. There exist solutions for ...
- 4,895
9
votes
5
answers
1k
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 ...
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