Questions tagged [fastq]
FASTQ is a file format use to store short reads and their quality values
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How can I detect MCPyV in a FASTQ file?
I have received two NGS files from an NGS company, both are FASTQ files that correspond to reads from a tumor sample. I heavily suspect that MCPyV is present, and I am hoping to identify it.
What ...
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Remove files after process is terminated
In my pipeline nextflow, I create a channel with channel.fromSRA and the channel contains lots of heavy files.fastq.gz. Then I have a first process to unzip files and transform them in files.fasta and ...
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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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Shell script to validate fastq issue
I have two GSM ID as test case where both of them are having data when I checked through sra explorer tool but when I try to fetch through a script only one of them returns output where the other one ...
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Parameter optimisation of minimap2
I'm leveraging minimap2 to map select genes from short-read microbial fastq metagenomics zip files.
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Compressing read data (converting fastq to fastq.gz) on Windows
I downloaded some of my data in fastq format instead of fastq.gz. I want to upload my data on a server now.
I was wondering if there is a way to convert my fastq files to fastq.gz on windows (I read ...
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I can't launch FastqCleaner I always get a warning message and the application never starts
I tried to install all the needed and related packages but I still did not know what the problem is, Can anyone please help if anything else I can do??
I always get this over and over:
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fastqCleaner failing to launch in RStudio
When I execute:
> FastqCleaner:::launch_fqc()()
I get the following output
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What are the output files of RNA-Seq from facility?
This question was also asked on Reddit
I am new in our lab and I am going to do bulk RNA-Seq. What type of files will we get from the company (Genewiz)? Will it be a bunch of Fastq files? or they give ...
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10X low rate of correct barcodes was observed for the candidate chemistry choices for the input
I am testing a 10x fastq dataset , but cellranger count complains "An extremely low rate of correct barcodes was observed for all the candidate chemistry choices for the input", I have tried ...
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How to determine NCBI's SRS google cloud bucket or AWS bucket
It appears that AWS and GCP host SRA data and it's beneficial to grab the data from that source when running on GCP for example.
Given an SRR accession like SRR1929796 https://trace.ncbi.nlm.nih.gov/...
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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 ...
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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 ...
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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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Good / recommended way to archive fastq and bam files?
We have a lot of Illumina sequenced exome data. Currently we are using spring for its great lossless compression, but we are looking if there is anything better (and most preferably opensource) which ...
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How to differentiate DNA fastq and RNA fastq files?
I have 2 sets of fastq files from another collaborator. The first is contains exome data and the second contains RNAseq data. But both have the RNA in the name but a different ID. How do I ...
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Running cellranger on scRNASeq data with feature barcoding (10x + antibody capture)
I can't seem to find a clear answer to this question, so here it goes:
I have sequenced scRNASeq + scVDJSeq (TCR) data, which has been sequenced using feature barcoding from 10x genomics, via antibody ...
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Can we test the accuracy of Phred scores shown in FASTQ files
Recently I have ran a human WGS on the BGI DNBSEQ system, and their FASTQ quality scores seem to be quite impressive, where the Phred scores barely deteriorate along the read length when checked on ...
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DNASTAR viral-host integration assembly keeps failing
I have two NGS files from an NGS company corresponding to the sequencing data from a tumor sample as follows:
TB_7710391_R1.FASTQ.gz
TB_7710391_R2.FASTQ.gz
I have downloaded the genome for MCPyV as ...
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How to get a file with the number of reads for several fastq.gz files?
I have generated several FASTQ files and I would like to know the amount of reads for each of them.
I am planning to run FastQC on the files which I know would give me the number of reads per sample ...
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If fastp output is not a good measure of FASTQ correctness, what is?
In the beginning of my pipeline, I just fed the paired reads (2 files) into fastp, with the default options, and assumed it would do a good job preparing the reads for the next step: alignment
But I ...
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Remove low quality reads
I want to remove reads from FASTQ file that contain homopolymers > 10bp and remove reads with <35 average quality score across the entire read.
To remove homopolymers > 10bp, I tried this on ...
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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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How can I edit a specific FASTQ read in place, given the read ID?
I am introducing SNVs into specific samples in order to estimate false negative rates for a variant calling pipeline. I know reads can be simulated but I would actually prefer to use the real data so ...
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Extract nanopore read ID & start times from fastq file
I have a fastq file from minION (albacore) that contains information on the read ID and the start time of the read. I want to extract these two bits of information into a single csv file.
I've been ...
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Calculating read average length in a Fastq file with bioawk/awk
I found here this awk script:
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CRISPR genome wide screen analysis using MAGeCK-- Loss of reads/sgRNA using MAGeCK count function?
Sorry if this question seems basic. I am trying to run the MAGeCK pipeline to analyze CRISPR knockout screen data produced by someone in my lab around 5 years ago. I was given the data as bam files ...
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Comparison of fastq files reads
My goal is to compare reads from two different fastq files on a Linux machine.
The following are the comparisons to perform:
How many common reads are between the two fastq files?
How many reads are ...
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What can be the bias of aligning paired-reads in a single-end mode?
I don't know if I'm in the right place but I have a technical problem to fix. I would have to align paired-end reads from Illumina sequencing to compare a normal genome with a tumor one.
When I align ...
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Sequence format: grouping sequences within a flat file
Is there a sequence format allowing multiple sequences to be grouped across a flat file? The specific application is stacking separate nucleotide sequences against a given RNA secondary structure.
To ...
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What is the difference between FASTA, FASTQ, and SAM file formats?
I'd like to learn the differences between 3 common formats such as FASTA, FASTQ and SAM. How they are different? Are there any benefits of using one over another?
Based on Wikipedia pages, I can't ...
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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?
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Aligning scRNA-seq fastq to .bam without cell barcodes
I would like to convert the fastq files from this dataset: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98679 to .bam files. The group did not provide the scripts they used to to their ...
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Converting .bw files to .fq (fastq)
I am able to convert .bw files to .fq(fastq) manually in Shell, but I would like to automate the process coz I have hundreds of .bw file that I need to convert. Till now, I could think of following ...
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Pipeline for paired end RNA sequence data to proteins
Forgive the basic question here, but I'm super novice at this ...
I have a series of paired-end RNA fastq files (e.g. SRR10720226_1.fastq.gz and ...
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Multiple file Python script
I am currently doing an analysis requiring a multiple-input script. I have a directory filled with 900+ samples.
Each sample is comprised of two-files in a fastq format. This is an example of a sample:...
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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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Determine reference for reference-compressed SRA file
Note: this question was also asked on Github.
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 ...
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How to convert CRAM file with 10x data in three fastq files
10x Genomics data are stored in three FASTQ files, besides the standard R1 and R2 reads, there is also a I1 file with some metadata. Sometimes however they are shipped in a single bam/cram file (e.g. ...
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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 are from viral or bacterial infection from human samples? Thanks in advance.
EDIT:
Looking at ...
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Fast way to count number of reads and number of bases in a fastq file?
I am looking for a tool, preferably written in C or C++, that can quickly and efficiently count the number of reads and the number of bases in a compressed fastq file. I am currently doing this using <...
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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 ...
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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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How to compare sequences of genes obtained after whole-genome sequencing to reference genome?
My idea is to align whole-genome sequencing data (as fastq files after, 30× coverage, gDNA) to the reference mouse genome (NCBI), extract the immunoglobulin locus and compare it to the reference. I ...
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When using cutadapt, can I specify an R2 adapter as optional when I have a required R1 adapter?
I'm using cutadapt 3.5 to trim adapters and perform some filtering on paired-end data.
Both R1 and R2 sequences have 3' adapters that might be found depending on the sequence length, but R1 also has ...
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Translate all reads in a .fastq into protein sequence from deep mutational scanning experiment
I'm working with paired-end NGS reads from an Illumina platform. The sequences I have are all of the same gene, but have one or more substitution mutations each.
Here is a rough workflow for ...
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How likely is it to find primers sequences in already-trimmed reads?
So, I am analysing 18S amplicon data (fastq files) to be able to eventually investigate the taxa composition.
After removing primers (using cutadapt) from both R1 ...
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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 ...
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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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