Questions tagged [fastq]

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

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Programmatic Access to `fastq-load.py` Arguments in SRR Metadata

Is there a way to programmatically access the fastq-load.py arguments from the SRR metadata? Specifically I would like to capture the exact command line arguments ...
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104 views

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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62 views

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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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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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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1answer
55 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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Could I create assembly by unicycler for ion torrent output?

I have ubam files from ion torrent machine, I convert it to fastq by samtools bam2fq tool, then I use galaxy platform to assembly the genome by Unicycler. At the end I get a fasta file. My question ...
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143 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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83 views

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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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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161 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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412 views

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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225 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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155 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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164 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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96 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, ...
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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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118 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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116 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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94 views

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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561 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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276 views

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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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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523 views

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 ...
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168 views

Fastqc- Per Base Sequence Quality

I am trying to figure out how to interpret the "Per Base Sequence Quality"? What does Position in reads (bp) mean? Also in order to draw this box-plot graphics, more than one quality scores are needed ...
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141 views

filter out FASTQ reads which are shorter

I tried to filter out FASTQ reads which are shorter than 259 bp with ...
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3k views

Calculating read average length in a Fastq file with bioawk/awk

I found here this awk script: ...
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fuse fastq files with multiple records

I'd like to fuse ~50 pairs of corresponding fastq files on per sequence bases. I'd be happy for a solution as a Linux script, R script (if feasible with huge files), or any free software that runs ...
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391 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: ...
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258 views

Counting repeated kmers sequences that match at least x % of reads sequence

Working on a fastQ file, I would like to get the occurrences of repeated sequences for all possible kmers of a given length that cover at least 90% of the read's length for the whole data set. ...
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278 views

How to get the count of each kmer past 255 using khmer

I have a Fastq file and I want to get the exact count of each possible kmer from this file. On a previous post called How to use khmer to count k-mers? Daniel Standage proposed a custom script based ...
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1answer
61 views

efficient counting of dinucleotides/trinucleotides on fastq reads?

What's an efficient way of counting of dinucleotides/trinucleotide pattern on fastq.gz file reads? I know there are tools like seqtk that will be very efficient at reading through the .fastq.gz files,...
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1answer
1k views

5' and 3' bias in Rna-seq data

I'm working with rna-seq samples. I see 5' bias and also 3' bias in the per-base sequence content plot. From this link I see that the bias at the start of the sequences appears to be the result of ...
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How to demultiplex pair-end fastq reads with barcode 2 in the identifier line?

I have multiplexed pair-end fastq reads with dual barcodes. The issue is that one barcode is present in the header and one is present at the beginning of the read. I need a method to demultiplex this ...
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1answer
101 views

Can the canu assembler output a fastq file of the final assembly just like HGAP4?

I have assembled some genome from Sequel PacBio data both with HGAP4 on the SMRT Link interface and using canu on the command line. The HGAP4 assembler outputs a fastq file of the final assembly such ...
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Canu assembly not making a single consensus?

I've downloaded reads from this BioProject. Using canu with default parameters (no correction), I've got 4 contigs, none of which really look like the reference plasmid here. The command I used was: ...
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776 views

Estimating BAM file from compressed fastq file size

Is there a way to estimate the size of a BAM file will have after mapping with BWA? The input file are two mates fastq files, compressed with gzip, each one about 70G.
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210 views

Is there a way to quickly verify the presence of some SNPs in Fastq files?

Is there a tool that can scan fastq files without assembling them for a custom list of user defined snps?
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1answer
260 views

Split FASTQ and matching BAM into matching chunks

I am running a slow downstream analysis on a large set of nanopore reads (approx 3 million), and would like to split them into smaller chunks, run the analysis in massively parallel, and then ...
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1k views

How to convert fastq to fast5

fast5 is a variant of HDF5 the native format in which raw data from Oxford Nanopore MinION are provided. You can easily extract ...
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437 views

How can I edit a specific FASTQ read in place, given the read ID?

Given a read ID, I want to edit a single basecall (e.g. the 12th base) for just that read from within a large FASTQ file containing millions of reads. example, i want to change the 12th base ('C') in ...
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692 views

FASTQC overrepresented sequences after trimming

I have a set of RNA-seq samples from different experiments (Single and Paired End, depending on the experiment). I ran FASTQC in all the samples and found overrepresented adapter sequences: I removed ...