Questions tagged [fastq]

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

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2 answers
401 views

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 ...
2 votes
1 answer
50 views

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/...
0 votes
1 answer
36 views

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 ...
0 votes
1 answer
316 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? ...
3 votes
1 answer
94 views

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:...
7 votes
5 answers
3k 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 ...
6 votes
1 answer
67 views

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 ...
1 vote
2 answers
155 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. ...
2 votes
5 answers
307 views

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 ...
1 vote
1 answer
103 views

fastqCleaner failing to launch in RStudio

When I execute: > FastqCleaner:::launch_fqc()() I get the following output ...
12 votes
8 answers
12k views

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 <...
4 votes
2 answers
7k views

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

I found here this awk script: ...
1 vote
0 answers
51 views

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 ...
2 votes
1 answer
190 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" ...
0 votes
2 answers
137 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 ...
1 vote
1 answer
78 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 ...
1 vote
0 answers
42 views

Bowtie2 gets stuck on alignment

I am aligning a fastq file as follows: ...
1 vote
0 answers
93 views

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: ...
39 votes
4 answers
49k views

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 ...
1 vote
1 answer
64 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 ...
0 votes
0 answers
48 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 ...
0 votes
1 answer
63 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 ...
6 votes
4 answers
6k views

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 ...
1 vote
1 answer
123 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 ...
7 votes
1 answer
425 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 ...
0 votes
1 answer
592 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 ...
1 vote
1 answer
949 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: ...
4 votes
3 answers
1k 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 minimap2 on the FASTQ files, resulting ...
0 votes
1 answer
40 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 ...
1 vote
3 answers
86 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 ...
0 votes
0 answers
64 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 ...
1 vote
2 answers
86 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 ...
1 vote
1 answer
329 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 ...
1 vote
2 answers
197 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 ...
20 votes
12 answers
2k views

Random access on a FASTQ file

I would like to select a random record from a large set of n unaligned sequencing reads in log(n) time complexity (big O ...
4 votes
1 answer
55 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.. ...
0 votes
1 answer
100 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 ...
2 votes
1 answer
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 ...
1 vote
2 answers
309 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?
4 votes
1 answer
160 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 ...
0 votes
0 answers
43 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?
1 vote
1 answer
41 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 ...
0 votes
1 answer
86 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 ...
3 votes
2 answers
280 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 ...
2 votes
1 answer
101 views

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

I have the following files: ...
0 votes
1 answer
266 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 ...
3 votes
0 answers
29 views

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 ...
2 votes
5 answers
1k 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 ...
20 votes
10 answers
5k views

What is the fastest way to calculate the number of unknown nucleotides in FASTA / FASTQ files?

I used to work with publicly available genomic references, where basic statistics are usually available and if they are not, you have to compute them only once so there is no reason to worry about ...
1 vote
3 answers
2k 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 ...