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Questions tagged [fastq]

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

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Aligning FASTQs to FASTA reference

I'd like to align some FASTQs to an average mtDNA FASTA file that I have downloaded so I can have the human mtDNA isolated from those FASTQs. For that, I used bowtie2. Can I expect that after running ...
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How to design a synthetic wastewater FASTQ file that could be flagged as "engineered"?

I am an apprentice-level python user who occasionally works in medical laboratories and mainly does business work. I am presented with the unenviable task of orchestrating a proficiency test of some ...
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Downloading multiple SRA files as FASTQ files using SRA Toolkit

I was able to download all of the SRA files for a specific bioproject using the command: prefetch -O output_directory --option-file SRR_Acc_List.txt I then tried ...
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Compare FASTQ reconstructions to mtDNA

I have some doubts in how to proceed to compare ancient mtDNA with modern mtDNA. A little more context: The problem: I have some FASTQs associated with a given FASTA. They contain mtDNA. My goal is to ...
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Aside from the header info, is there any way to distinguish between sequences generated by MiSeq and MiniSeq platforms?

I am comparing Illumina MiSeq (using MiSeq v3 kit) and MiniSeq (MiniSeq High Output kit) instruments for sequencing E.coli and Salmonella. I am curious if there is any way to bioinformatically ...
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How to know if FASTQ/BAM is from reference genome (FASTA)?

I'm new to bioinformatics. I have a problem in which I have a FASTA reference genome and lots of reads in FASTQ files. Some of them could be contaminants, so I'd like to filter them out and get only ...
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Fastq file with very high per base sequence quality and no box-whisker plot

I have my data from NCBI. I am having difficulty making sense of and correlating my fastq file read 1 and read 2 and the fastQC report. As shown below, I have two paired-end read results each ...
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Discrepancy in Read Counts Between FastQ and BAM Files in Adapter-Trimmed Pipeline

In a FastQ to BAM pipeline where only adapter trimming is performed, I've noticed a potential discrepancy in read counts between the initial FastQ files and their resulting BAM file. Specifically, I'm ...
papabiceps's user avatar
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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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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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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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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 ...
Sina Asadi's user avatar
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5 answers
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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 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 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 ...
pythonbeginner's user avatar
2 votes
1 answer
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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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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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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 ...
Cassie Bishop's user avatar
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1 answer
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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 ...
cucalorda's user avatar
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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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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 ...
Angus Campbell's user avatar
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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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1 answer
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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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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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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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fastqCleaner failing to launch in RStudio

When I execute: > FastqCleaner:::launch_fqc()() I get the following output ...
Leon Lenzo's user avatar
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2 answers
467 views

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 ...
abc's user avatar
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1 answer
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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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Bowtie2 gets stuck on alignment

I am aligning a fastq file as follows: ...
justinian482's user avatar
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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: ...
Ruba Mahmoud's user avatar
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1 answer
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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 ...
Paul's user avatar
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1 answer
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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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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 ...
gabt's user avatar
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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 ...
Justin1609's user avatar
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1 answer
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How to convert multiple single-end bam files to fastq using samtools

Hi I am trying to convert bam files generated from Ion Torrent Proton sequencing to fastq format so that I can upload them to ...
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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? ...
Greater's user avatar
1 vote
3 answers
4k views

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 ...
Tarannom's user avatar
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1 answer
127 views

Impact of merging ChIP-seq runs of the same sample on PCR duplicates identification?

I'd like to a follow up question to this question related to merging fastq files for ChIP-seq. Let's assume we have one sample library that is re-sequenced two or three times in order to achieve a ...
Ni-Ar's user avatar
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1 vote
2 answers
376 views

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. ...
1 vote
3 answers
225 views

Finding smaller sequences from within larger sequences

I am currently working with fastq files which have hundreds of thousands of lines of text. However, not all of them are sequences I am interested in. My sequences are in one line and have a fixed ...
Jean Luc's user avatar
2 votes
2 answers
503 views

Get frequency of index sequences of fastq file

I recently did some sequencing on a MiniSeq and unexpectedly the Undetermined_S0_L001_R1_001.fastq.gz file contained quite a lot of data (about 40% of total). I ...
justinian482's user avatar
1 vote
1 answer
810 views

How to convert txt.gz into fastq.gz?

I'm a newbie to bioinfo. I'm trying to use galaxy.networkanalyst.ca for the analysis of RNA-Seq data and for that I need to convert txt.gz files into fastq.gz files. Link: GSM4273445 is one sample ...
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