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Removing adapters + primers from fastq files

I am currently in the process of removing adapters and primers from some 16S data acquired, and have a conceptual question regarding this pre-processing step: So there are a series of different primer ...
h3ab74's user avatar
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1 vote
1 answer
1k views

Searching for adapter sequences in FASTQ files - metgenomics

I have recently received some metagenomic data from 16S rrna sequencing. The sequencing company claim to have removed primers, however not adapter sequences. Please note that the files have been ...
h3ab74's user avatar
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427 views

tmhmm installation and running

I am trying to predict transmembrane protein using tmhmm-2.0c. According to Package instruction, I have changed the path of perl inside the program like as ...
Kishor Kumar Sarker's user avatar
1 vote
1 answer
49 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 ...
Lafayette's user avatar
  • 113
0 votes
2 answers
202 views

Changing this code in a way to work for my files

I have a bash script which extracts some information from a .vcf file but one .vcf file at each time. How I can change this script in a way to work on a bunch of .vcf files and the output is a .txt ...
Zizogolu's user avatar
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0 votes
2 answers
135 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 ...
user avatar
0 votes
1 answer
122 views

How to debug a bash script

Please somebody debug my code In sub-folders there are 500000 vcf files from which I only need 500 vcf files listed in ...
Zizogolu's user avatar
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0 votes
2 answers
197 views

How to find restriction enzyme frequency in whole genome and count the distance between them?

I am having possibly a simple question which is proving difficult. My objective is to take the reference FASTA file and flat file database with 1500 restriction enzymes with its cutting sites (mostly ...
Santosh's user avatar
0 votes
1 answer
1k views

How to convert mzXML to mzML format (mass spectrometry files)?

How to convert mzXML to mzML format (mass spectrometry files) preferably under Linux and/or Python?
Soerendip's user avatar
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0 votes
1 answer
135 views

Error when using awk command to trim sequence files

I am attempting to edit my fastq sequence files with an awk command from a published article. The sequence files are all ...
Justin1609's user avatar
0 votes
2 answers
215 views

Looping over several files in bash

I have a bash script: I am wondering how I can change this script to loop over a bunch of .vcf files and give output .txt with the name of corresponding .vcf I tried changes done in similar script ...
Zizogolu's user avatar
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0 votes
1 answer
997 views

Converting Fastq files to Fasta files on Ubuntu

I am new to bioinformatics and programming. I tried to convert my fastq files to fasta file, but got this. What could be wrong? ...
Greater's user avatar
0 votes
2 answers
506 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: ...
MicroBiostat's user avatar
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1 answer
1k views

VCF-merge fails due to tabix not producing .tbi files

I'm trying to use vcf-merge to combine 2 exome capture vcf files (~250K and ~330K in size) before trying it on all 96 samples. I'd appreciate any advice on the best way to do that! I've detailed what ...
Brian's user avatar
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0 votes
2 answers
32 views

Assemble Anaeroplasma species genome from metagenomic PacBio data

I have a fasta file containing reads generated by PacBio HiFi whole genome sequencing of a feces sample from mouse. I would like to use this dataset to generate an assembled circularized genome for an ...
Amroon's user avatar
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1 answer
348 views

BEAGLE do not see and/or not use OpenCL

I am conducting phylogeny analyses using BEAST 2 as software tool. It is said that it can be accelerated by BEAGLE-library. I have a personal laptop with Windows & a cluster with CentOS. I ...
Vovin's user avatar
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0 votes
2 answers
1k views

Using grep to get lines from a file (.tsv) that contain specific samples listed in a sample file (.tsv)

So I have a file, let's call it pcawg.tsv. It's formatted like the one down below. ...
Michelle Yang's user avatar
0 votes
1 answer
1k views

Cellranger gives error

I am trying to run cellranger but I get fastq permission denied error ...
Zizogolu's user avatar
  • 2,160
0 votes
1 answer
2k views

How to generate ultrametric phylogenetic trees?

This question has also been asked on Biostars I am going to use ultrametric tree for downstream analysis. I would like to see use the ultrametric tree for Ranger-DTL for infer gene family evolution by ...
Kumar's user avatar
  • 109
0 votes
1 answer
40 views

Replacing some strings in R or terminal

I have a .txt file; I have 139 unique sample IDs in sampleID column ...
Zizogolu's user avatar
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0 votes
0 answers
33 views

How to access specific SRA sequences within an SRP file?

How do you get a specific 100 SRA sequences from a Bioproject which contains 400 runs, when you don't need all of them?
K_081's user avatar
  • 149
0 votes
1 answer
75 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 seperate file such as file1.txt. I want to change all other files by using this file1.txt based on a matching string. for ...
Umar's user avatar
  • 135
0 votes
0 answers
138 views

Locate the saved template of minknow

I am using minknow on ubuntu. After saving the template (settings), where is that file locally stored in the system? Also what is its format/extension?
K.Harini's user avatar
-1 votes
2 answers
840 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: ...
stack_learner's user avatar
-1 votes
1 answer
137 views

computing the distance between ( XYZ coordinates)

I have a txt file (50k) proteins in it, which looks like this: line 1:the protein code line 2: protein length in amino acids line 3: amino acid sequence line 4: secondary structure line 5: XYZ ...
Amal's user avatar
  • 81
-1 votes
1 answer
79 views

stats.sh error in BBmap package

I am trying to calculate the N50 value from the assembled FASTA file. I used stats.sh from the BBmap package. I executed the following command ...
seq's user avatar
  • 9
-1 votes
1 answer
470 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 ...
Mollie Passacantando's user avatar
-1 votes
1 answer
48 views

DNA seq cutting using Linux [closed]

I need to use the cut command on a human insulin sequence row wise but i don't know the command.I already ran byte wise command but the gave me column wise results. I cant use the -f option since i ...
Nargis Naqvi's user avatar

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