Questions tagged [fastq]

FASTQ files are used in bioinformatics to store sequence information and sequencing quality scores.

FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity.

[Wikipedia]

257 questions

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1 answer

How to loop over multiple folders to concatenate FastQ files?

I have received multiple fastq.gz files from Illumina Sequencing for 100 samples. But all the fastq.gz files for the respective samples are in separate folders according to the sample ID. Moreover, I have multiple (8-16) R1.fastq.gz and R2.fastq.gz…

asked Feb 23 '22 at 19:57

Anik Dutta

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1 answer

Exception in thread "main" java.awt.HeadlessException

I am running a program FASTQC in the command line(Ubuntu terminal on windows 10 PC) but got the error of the following. I am not sure how to solve this and I would appreciate it if some one already know the solutions. Exception in thread "main"…

ubuntu fastq

asked Nov 24 '21 at 14:14

adR

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0 answers

Converting BAM files to FASTQ using Google Colab

I am trying to convert BAM files from Ion Amplicon sequencing to FASTQ files. I am using Google Collaboratory. I will be using the FASTQ files in R for the pipeline DADA2. Any help would be greatly appreciated.

r google-colaboratory bioinformatics fastq bam

asked Nov 04 '21 at 09:11

Nicole_B

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1 answer

How to search and replace using Regex s/ when having to convert genome quality to ASCII?

I am struggling to convert a genome read quality from a fasta.qual file (40, 39, 38 etc) to ASCII using Phred+33 on Perl, but can't get it to work. I am trying to do it through the s///g operator. I have my qualities stored in a hash and I am trying…

regex perl bioinformatics fasta fastq

asked Oct 31 '21 at 15:10

Alan

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1 answer

Concatenate multiple sets of 2 fastq files in BASH

I'm trying to merge multiple sets of 2 fastq files from the same sequencing library. I have a txt file with all the sample names in it. The samples were sequenced in paired-end so there're both _1.fastq.gz and _2.fastq.gz files associated with each…

bash for-loop bioinformatics cat fastq

asked May 18 '21 at 20:29

Michelle Lu

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0 answers

How to extract a part of a sequence from FASTA

I have FASTA files, from an in vitro SELEX experiment. All reads should in theory start with the same 6 bases (core seq: GCTGCT) and be of equal length - 27nt. In reality, some reads start even 10 bases later with the core sequence and continue with…

python r fasta fastq

asked Mar 23 '21 at 15:41

Fluorine

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1 answer

How can I create a FASTQ sequence file?

I have a genomic database, which contains a simple character sequence (like >chr1 AGTGTCA.....). Now, I want to convert it to the standard FASTQ format like this: @HWUSI-EAS594-R:1:3:1453:1350#0/1…

bioinformatics fastq

asked Jul 10 '11 at 01:14

Arpssss

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2 answers

Bash loops instead VS parallel processes

I wrote a simple script using cat+pipe+parallel in bash but due to the large amount of input data (>200) my computer crashes. However, it works well with only few files (2). I was recommended to use "for" or "foreach" loops instead to avoid the…

loops parallel-processing fastq

asked Feb 05 '21 at 08:22

Valentina

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1 answer

Why is my R function not running? Trying to send R script to cluster

This is a very beginner question, so thanks in advance. I was given an R script to align from fastq files to a genome. All I need to do is sent this R script to my uni's cluster, but I want to make sure the script is running fine on my own computer…

r function bioinformatics fastq rna-seq

asked Jan 04 '21 at 20:06

kefir

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1 answer

Hot to trim every nth line by a different value?

I would like to trim the last XY characters of every 4th line. The cut off should be the different between the character count from line 4 and 2, and line 8 and 6. For example: line 4 (29 characters) - line 2 (20 characters) = 9. So the last 9…

awk trim cut fastq

asked Dec 17 '20 at 14:42

gnikixam

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3 answers

awk; getting multiple lines from two files when they share a common header

I have a question that is quite similar to many other questions regarding this topic, yet I am unable to extent these solutions to the exact output I am looking for. I have two files that are formatted in fastq style, which looks like…

awk fastq

asked Dec 02 '20 at 13:04

MostlyHarmless

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2 answers

How to remove a SeqRecord object from a fastq file

I have a parsed fastq file, and I am doing some operations with the reads. Concretely, I am trying to determine if my fastq files have reads that belong to a microorganism contamination, instead of my human sample. So, if my read is a contamination,…

python parsing biopython fasta fastq

asked Nov 24 '20 at 19:46

Begoña Sánchez Aliena

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2 answers

How to sort dirty fastq files to interleaved fastq

I have a fastq file (file.fastq) of about 80GB in size which has a header line and three subsequent information lines. I need to match /1 and /2 in header lines matching the header information and put them in one file sorted by /1 and /2…

linux bash shell awk fastq

asked Nov 05 '20 at 18:37

MAPK

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In a fastq file, how do I change the sequence headers to the file name and a unique identifier?

I'm working with barcoded data and I want to be able to combine the fastq files and easily be able to tell which barcode the read originally had. So I am trying to change the names of the reads to the name of the file (i.e barcode01.fastq) and…

bash awk fastq

asked Oct 14 '20 at 23:52

DewBudd

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1 answer

Combine multiple wildcards in Snakemake

├── DIR1 │ ├── smp1.fastq.gz │ ├── smp1_fastqc/ │ ├── smp2.fastq.gz │ └── smp2_fastqc/ └── DIR2 ├── smp3.fastq.gz ├── smp3_fastqc/ ├── smp4.fastq.gz └── smp4_fastqc/ I would like to count the number of reads by sample and…

python snakemake fastq

asked Sep 14 '20 at 11:46

Elysire

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