Questions tagged [fastq]

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

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41 views

fastqCleaner failing to launch in RStudio

When I execute: > FastqCleaner:::launch_fqc()() I get the following output ...
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108 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 ...
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35 views

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: ...
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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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1answer
52 views

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 to determine SRR google cloud bucket or AWS bucket

It appears that AWS and GCP hosts 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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44 views

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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1answer
37 views

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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1answer
70 views

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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1answer
151 views

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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1answer
255 views

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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1answer
19 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 ...
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103 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. ...
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81 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 ...
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60 views

Could one Align a FastQ data to a reference genome

I need help with the following question : Given a FastQ data what can we do directly with it ? Assess it for Quality control Align it to a reference genome Call variants Assemble's genome My Thoughts ...
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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 ...
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1answer
236 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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1answer
68 views

Demultiplexing FASTQ file without index information

I am trying to understand how data that was uploaded to SRA (https://www.ncbi.nlm.nih.gov/sra?LinkName=biosample_sra&from_uid=4510743) can be analyzed with the assumption that the FASTQ file ...
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1answer
54 views

Telling grep to treat N as [ATCG]

Okay so I'm using grep to try and get a preview of some trimming operations that are not going as expected.. Lets say that my sequence in the FastQ file is: ATNGCNATCG What I want to do is.. ...
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2answers
139 views

Fastq: how can I check if they are from DNA or RNAseq data?

I have (gave me) Illumina fastq files, which I want to use for variant calling, and I do not know if they are DNAseq or RNAseq data. How can I check this? I do not have any report or who to ask. Many ...
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41 views

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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1answer
112 views

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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1answer
39 views

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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1answer
59 views

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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1answer
63 views

Merging several fq.gz files or R1 and R2 classes into a single one

I have the following files: ...
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1answer
163 views

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 [closed]

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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182 views

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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719 views

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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3answers
1k views

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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79 views

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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1answer
207 views

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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175 views

FASTQ file trimming

I have a FASTQ file: ...
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99 views

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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2answers
203 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
830 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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1answer
216 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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1answer
115 views

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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1answer
102 views

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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2answers
138 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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2answers
70 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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4answers
2k 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
73 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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1answer
53 views

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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2answers
819 views

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
279 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
1k 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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0answers
137 views

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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285 views

Does this FASTQ data contain single or paired end calls?

I have this fastq data from GEO: ...