Questions tagged [fastq]

FASTQ is a file format use to store short reads and their quality values

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How do you determine the strandedness of a RNAseq dataset? [duplicate]

How do you verify if a RNAseq dataset is unstranded, stranded or revesely stranded from a fastq file?
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Find pattern that is present twice and allow <=2 mismatches on each

I have a fastq file of 400,000 reads (so speed is important). In the sequences there are barcodes integrated that should be present twice. Given a barcode, I want to find the sequences that have the ...
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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 ...
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Nvidia Parabrick fq2bam pipeline error - No such file or directory

I am trying to implement Nvidia-parabrick fq2bam pipeline to process my WES dataset. The reason for opting this pipeline is the huge number of samples (1004) which take many months to process for ...
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Merging several fq.gz files or R1 and R2 classes into a single one

I have the following files: ...
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1answer
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How to find the number of contigs produced? N50 length in base pairs? N90 length in base pairs?

I am having trouble with some underlying questions about my project. I have ran a Trinity tool to create a trinity.fasta file. To determine some underlying questions, I used the utility asm_stats to ...
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Template files for bioattributes and meta-data

I am in process of submiting my FASTQ files to the SRA database. I am a little confused about how to fill the biosample attributes and SRA metadata. I would really appreciate if you anyone could share ...
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Can I eject the flow cell MinION from USB port when doing basecalling?

Can I eject the flow cell MinION from USB port when doing basecalling? Because its taking long and its not possible to wait for its finished, will it affects basecalling?
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Extract Illumina reads that match with respect to their coordinates on the genome from fastq files

I want to use BPP to estimate divergence times and population sizes of a set of species. I have a vcf file with SNPs called from RADseq. The problem is that BPP uses the multi-species coalescent model ...
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How to measure the total size of a fastq file in base pairs?

Or Kbps/Gbps. It feels like it should be conceptually very simple, but I can't seem to figure out the right combination of keywords to find it via my search engine. Help would be appreciated! I have ...
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Download multiple fastq files using fastq-dump

I want to download the following fastq files at the same time in Salmon: - SRR10611214 - SRR10611215 - SRR10611215 - SRR10611216 - SRR10611217 Is there a way ...
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nanopore QC measures on fastq file

I am working with virus nanopore sequencing data. I have to remove host genome from the reads. I want to run the QC on the fastq file after host genome subtraction. I have used nanoplot. It is slow. I ...
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Bash script for automatic overlap merging of respective paired-end reads from samples

I have around 300 paired-end files from 150 samples (1 forward and 1 reverse read for each sample). I want to merge (by sequence overlap) respective forward and reverse reads for each of the samples. ...
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131 views

FASTQ file trimming

I have a FASTQ file: ...
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Unable to gunzip fastq files from ENA

I am trying to process fastq files in order to build gene co-expression networks (by following this tutorial). When I download any fastq file from ENA, and try to process it with the command: ...
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96 views

Extracting specific sections from FASTQ determined by positions

Given a FASTQ file, I'd like to generate a new FASTQ file including only certain subsections of the original sequences specified by their positions. For example, say I want to extract the ...
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1answer
358 views

How to split FASTQ reads without re-running `fastq-dump`?

I downloaded a few FASTQs from the SRA that were paired-end 76 bp. When I look at the FASTQs, I get something like this: ...
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101 views

What is a proper way for random subsampling of metagenomic data?

Let's say we have a metagenomic sample that is paired-end FASTQ files including 10,000,000 DNA reads collected using shotgun sequencing. How would one make a random subsample of the mentioned ...
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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 ...
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Filtering raw sequencing reads

I have to filter the raw sequencing reads based on the following criteria: Remove reads containing adapters Remove reads containing N > 10% (N represents base that could not be determined) Remove ...
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Why does this naive Python paired Fastq reader work?

I wrote some throwaway code for ingesting paired-end reads from a Fastq file into memory. ...
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Is the quality score of fastq used somewhere besides trimming/fastqc?

In the fastq format every 4k+4-th line contains the positionwise qualityscore (ascii encoded): ...
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4answers
803 views

Convert FASTA to FASTQ with dummy quality scores

I have a FASTA file which I would like to convert into FASTQ format as the tool I want to use my data in requires it in FASTQ format. So dummy quality scores are fine. Note: I am not using any ...
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1answer
55 views

Tool for calibrating base quality scores?

A given sequencing machine assigns a 'certainty' to each base call in the form of a per-base quality score (FASTQ format). I have reads from several machines aligned to the corresponding reference (...
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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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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: ...
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205 views

SRA Toolkit execution problem

I am trying to install SRA Toolkit on MacOS, following all the instructions from NCBI website. It is installed but fastq-dump cannot be executed because "cannot execute binary files". I tried "chmod +...
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1answer
891 views

Fasterq-dump: --split-spot or -concatenate-reads?

After using files that I downloaded from the SRA with fasterq-dump, I realize I am not 100% sure that I have all the data. I noticed in my downstream analysis that I seem to be missing the .1 and .2 ...
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Nanopore FASTQ header specifications

Is there a specification anywhere for how a Nanopore FASTQ header should be formatted? I am creating strategies for generating test FASTQ files and would like to ensure I am generating "correct" ...
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Does this FASTQ data contain single or paired end calls?

I have this fastq data from GEO: ...
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How to convert a .fastq chip-seq file into a wig/bigwig track and how to extract chip-seq peaks?

I have a reference .fasta file and a raw .fastq file with chip-seq data. I am trying to create a bigwig track from the and .fastq and .fasta ref file of the raw signal. Then I would like to do some ...
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181 views

How to remove degenerate sequence (N4) at the 5' and 3' of the reads?

I have to analyse GSE114327. For that, I use GSE instruction based on GSM3139597. In that data processing section has written: FASTQ reads were subjected to adapter removal (cutadapt) per ...
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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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Convert BAM to properly paired FASTQ files

I thought I had figured this one out. But apparently not. I need to convert a BAM file of paired-end alignments to two FASTQ files of paired reads to realign them, with a twist: I only want reads ...
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535 views

What do the FASTQ file names mean here?

I would like to run an analysis on Nanopore data. I'm trying to download sample data from https://github.com/nanopore-wgs-consortium/chm13. I would like to run minimap on the FASTQ files, resuling in ...
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197 views

Fast processing of fastq data

I am trying to write python script for customized filtering for fastq file (size >3 GB). My proposed script is as follows: ...
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Determine reference for reference-compressed SRA file

I have 241 SRA files that appear to be reference compressed. I didn't even know this was a thing until I tried to convert them to Fastq files without an internet connection. I got the "name not found ...
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224 views

Frequency of specific viral sequence in .BAM or .fastq

I was wondering if anyone had any experience 'counting' the frequency of a particular viral sequence in an individual's fastq sequence. So basically, counting the number of occurrences of a particular ...
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Testing for viral/bacterial infection FASTQ files

What's the best way to test if a pair of Illumina FASTQ files from blood DNA extraction contain any reads from viral/bacterial infection from DNA in human blood? Thanks in advance. EDIT: Looking at ...
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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, ...
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“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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2answers
187 views

Getting data from fastq by generator

I have a task in a training that I have to read and filter the 'good' reads of big fastq files. I downsampled, got the code working, saving in a python dictionary. But turns out the original files ...
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163 views

Where to Download Cancer Raw Reads (fastq)?

Does anyone know where I can download cancer raw reads (fastq files), tumor and Germline for non-humans? I wanted to make a study with human data but I don't have the control access to download raw ...
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Non-random access on a fastq file

There was a nice question on random access on a fastq file, however I have the opposite problem. I want to programatically access non-random fastq entries quickly (using C++). Say I have several ...
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606 views

Why does this human bam file only have one copy of each chromosome?

As we know that in human DNA sequence, one copy of chromosome comes from mother's DNA and another copy comes from father's DNA so as to form two copies of each chromosome in human DNA. So, if we ...
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Multithread fastq processing with kseq.h in C++11?

Background I am using the wonderful kseq.h as my fastq/fasta parser for a C++ project. My actual implementation uses something like this, where I am counting kmers ...
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1answer
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Are there free cloud computing platforms for biology projects? [duplicate]

I want to implement the analysis found in the paper RNA-Seq of Tumor-Educated Platelets Enables Blood-Based Pan-Cancer, Multiclass, and Molecular Pathway Cancer Diagnostics The project id is 281708. ...
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Delete all 4 lines of a fastq read from a fastq file using read ID

I have the following error when running bowtie2: Error: Read HWI-D00466:116:CC62WANXX:3:1102:7363:63646 1:N:0:GCACACG has more read characters than quality values. I now want to remove all 4 ...
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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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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 ...