Questions tagged [fastq]
FASTQ is a file format use to store short reads and their quality values
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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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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
...
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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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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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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 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 ...
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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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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?
...
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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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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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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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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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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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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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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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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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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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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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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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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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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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Merging several fq.gz files or R1 and R2 classes into a single one
I have the following files:
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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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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 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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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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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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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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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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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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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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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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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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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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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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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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